Chlamydia pneumoniae polypeptides and uses thereof

ABSTRACT

The subject of the invention is the genomic sequence and the nucleotide sequences encoding polypeptides of  Chlamydia pneumoniae , such as cellular envelope polypeptides, which are secreted or specific, or which are involved in metabolism, in the replication process or in virulence, polypeptides encoded by such sequences, as well as vectors including the said sequences and cells or animals transformed with these vectors. The invention also relates to transcriptional gene products of the  Chlamydia pneumoniae  genome, such as, for example, antisense and ribozyme molecules, which can be used to control growth of the microorganism. The invention also relates to methods of detecting these nucleic acids or polypeptides and kits for diagnosing  Chlamydia pneumoniae  infection. The invention also relates to a method of selecting compounds capable of modulating bacterial infection and a method for the biosynthesis or biodegradation of molecules of interest using the said nucleotide sequences or the said polypeptides. The invention finally comprises, pharmaceutical, in particular vaccine, compositions for the prevention and/or treatment of bacterial, in particular  Chlamydia pneumoniae , infections.

This application is a divisional of U.S. application Ser. No.09/198,452, filed Nov. 23, 1998 (now U.S. Pat. No. 6,559,294), whichclaims priority from U.S. application Ser. No. 60/107,078, filed Nov. 4,1998 (now abandoned).

The Sequence Listing for this application is on duplicate compact discslabeled “Copy 1” and “Copy 2”. Copy 1 and Copy 2 each contain only onefile named “seqlist-28Jul. 2001.txt” which was created on Jul. 30, 2001.The file is 5,284 KB. The entire contents of each of the computer discsare incorporated herein by reference in their entireties.

The subject of the invention is the genomic sequence and the nucleotidesequences encoding polypeptides of Chlamydia pneumoniae, such ascellular envelope polypeptides, which are secreted or specific, or whichare involved in metabolism, in the replication process or in virulence,polypeptides encoded by such sequences, as well as vectors including thesaid sequences and cells or animals transformed with these vectors. Theinvention also relates to transcriptional gene products of the Chlamydiapneumoniae genome, such as, for example, antisense and ribozymemolecules, which can be used to control growth of the microorganism. Theinvention also relates to methods of detecting these nucleic acids orpolypeptides and kits for diagnosing Chlamydia pneumoniae infection. Theinvention also relates to a method of selecting compounds capable ofmodulating bacterial infection and a method for the biosynthesis orbiodegradation of molecules of interest using the said nucleotidesequences or the said polypeptides. The invention finally comprises,pharmaceutical, in particular vaccine, compositions for the preventionand/or treatment of bacterial, in particular Chlamydia pneumoniae,infections.

Comparative analysis of the sequence of the gene encoding the ribosomal16S RNA has been widely used for the phylogenetic study of prokaryotes.This approach has made it possible to classify the Chlamydiae among theeubacteria, among which they represent a well-isolated group, with,nevertheless, a very weak link with the planctomyces. The Chlamydiaethus exhibit some unique characteristics within the eubacteria, inparticular their development cycle and the structure of their membranes.They have a unique two-phase cell cycle: the elementary body, a smallextracellular form, attaches to the host and is phagocytosed; in thephagosome, it is converted to the replicative intracellular form, thereticulate body. The Chlamydiae are obligate intracellular bacteriawhich multiply in eukaryotic cells at the expense of their energyreserves and nucleotide pools; they are responsible for a wide varietyof diseases in mammals and birds. The Chlamydiae are the only members ofthe order Chlamydiales, of the family Chlamydiaceae and of the genusChlamydia. Within the genus Chlamydia, four species are currentlydescribed: Chlamydia trachomatis, Chlamydia psittaci, Chlamydiapneumoniae and Chlamydia pecorum. These bacteria are grouped togetherand share biological and biochemical properties. Among them, only thefirst three infect humans, Chlamydia pecorum being a pathogen ofruminants.

The species Chlamydia psittaci infects many animals, in particularbirds, and is transmissible to humans. It is responsible for a typicalpneumonia, for hepatic and renal dysfunction, for endocarditis and forconjunctivitis.

The species Chlamydia trachomatis is the best characterized. Besides amurine strain, it is divided into two groups which are distinguishableby the nature of the diseases for which they are responsible: trachoma,genital attack and venereal lymphogranulomatosis. There are fifteenhuman serotypes of Chlamydia trachomatis (A, K) and LGV (L1, L2, L3).Strains A to C are mainly found in eye infections, whereas strains D toK and LGV are essentially responsible for genital entry infections. Itshould be mentioned that the LGV strains are responsible for systemicdiseases. Historically, it was in 1906 that Halberstaeder and VonProvaseck discovered, in trachoma patients, the presence of inclusionsin the cytoplasm of the cells derived from conjunctival scrapings. In1940, Rake and Jones described these same inclusions in certain cellsobtained by puncturing the ganglia from a patient suffering fromvenereal granulomatosis. Characterization of the Chlamydia trachomatismicroorganism was only successfully carried out in 1957, after a seriesof isolations in cell cultures.

It was in 1983 that Chlamydia pneumoniae was recognized as a humanpathogen (Grayston J T et al., 1986); since then, special attention hasbeen paid to this bacterium and it is estimated (Gaydos C A et al.,1994) that 10% of pneumonias, and 5% of bronchitides and sinusites areattributable to Chlamydia pneumoniae (Aldous M B et al., 1992). Morerecently, the association of this bacterium with the pathogenesis ofasthmatic disease and of cardiovascular impairments is increasingly ofinterest.

Serological studies have made it possible to observe that Chlamydiapneumoniae infection is common in children between 5 and 16 years ofage. Before this age, it is rare to find antibodies; the increase in thenumber of individuals carrying antibodies is then correlated with age upto 20 years. Accordingly, 50% of adults are carriers of antibodies, itbeing possible for this prevalence to be as high as 75%. These figuresare all the more striking since a first infection induces antibodylevels of which the persistence over time is limited to 3 or at most 5years, which suggests frequent reinfection during the entire lifespan.The annual seroconversion rate is about 8% between 8 and 12 years andabout 6% between 12 and 16 years (Haidl et al., 1994). Before the age of15 years, the seroprevalence of the disease is identical between bothsexes. After this age, men are more frequently infected than women; thisis true in all regions worldwide where such studies have been carriedout.

These infections are geographically highly widespread, as shown bynumerous studies carried out throughout the world (Kanamoto Y et al.,1991; Tong C Y et al., 1993). Developed countries of the north such asCanada, Denmark and Norway have the lowest infection rates; conversely,the highest prevalence rates are found in the less developed countriesof tropical regions where the infection may occur before the age of 5years.

Humans are the only known reservoir for Chlamydia pneumoniae and it isprobable that the infection is caused by direct transmission,respiratory secretions probably being responsible for this low-yieldtransmission (Aldous et al., 1992). The chain of transmission may alsoappear to be indirect (Kleemola M et al., 1988), suggesting that theinfection is caused by an effective transmission, but also thatasymptomatic carriers exist, which could explain the high prevalence ofthe disease. Other studies (Mordhorst C H et al., 1992) show that theefficiency of the transmission varies according to the individuals andlist cases of infection affecting all or the majority of members of onefamily or of a group of families. The period of incubation is severalweeks, significantly longer in this regard than that of many otherrespiratory pathogenic agents. Although under conditions of highrelative humidity the infectivity of Chlamydia pneumoniae in the openair decreases rapidly, suggesting a direct mode of transmission underthese conditions, it is probable that the transmission occurs in somecases indirectly since the microorganism can survive for up to 30 hoursin a hostile environment (Falsey et al., 1993).

Clinical manifestations due to Chlamydia pneumoniae are essentiallyrespiratory diseases. Pneumonia and bronchitis are the most frequentbecause they are clinically patent: since etiological diagnosis isevoked in this case, the infectious agent is identified. Theasymptomatic diseases are probably numerous (Grayston J T et al., 1992;Grayston J T et al., 1986; Thom D H et al., 1990). The disease thenprogresses via bronchitis or pneumonia; fever is absent at the time ofexamination but is sometimes reported by the patient. The degree ofseriousness of the disease is variable and in hospitalized patients, itis common to observe pleural effusion; a generalized infection may alsobe observed and, in severe cases, anatomicopathological examinationshows Chlamydia pneumoniae diseases.

Other syndromes such as sinusitis (Hashiguchi K et al., 1992), purulentotitis media (Ogawa H et al., 1992), or pharyngitis (Huovinen P et al.,1989) have been described, as well as infections with respiratoryimpairments similar to asthma (Hahn D L et al., 1991). Chlamydiapneumoniae has also been associated with sarcoidosis, with erythemanodosum (Sundelof et al., 1993) and one case of Guillain-Barre syndromehas even been described (Haidl et al., 1992). The involvement ofChlamydia pneumoniae in Reiter's syndrome has also been evaluated (BraunJ et al., 1994).

The association of Chlamydia pneumoniae with coronary diseases and withmyocardial infarction was first suspected from the observation of thehigh antibody level in 71% of patients having a heart disease (Shor A etal., 1992; Kuo C C et al., 1993; Puolakkainen M et al., 1993; Thomas G Net al., 1997). Studies carried out in several countries have shownsimilar results in patients with atheromatous impairments (Shor A etal., 1992; Kuo C C et al., 1993; Puolakkainen M et al., 1993; Grayston JT et al., 1996; Casas-Ciria J et al., 1996; Thomas G N et al., 1997;Jackson L A et al., 1997) and in patients with carotid impairments.Anatomicopathological and microbiological studies have detectedChlamydia pneumoniae in the vessels. The electron microscope has made itpossible to visualize the bacterium (Ladany S et al., 1989), which hasin fact been demonstrated by other techniques such as PCR (Campbell L Aet al., 1992; Kuo C C et al., 1993; Kuo C C et al., 1988). It alsoappears that the bacterium is more frequently found in old atheromatouslesions. Other studies carried out on young subjects from 15 to 35 yearshave given the opportunity to study the coronary arteries of peoplewithout atherosclerosis, this observation not being possible in oldersubjects (the onset of the atheromatous disease is early). In theseyoung subjects, the PCR studies did not find Chlamydia pneumoniae insubjects free of atheromatous disease, but revealed the presence ofChlamydia pneumoniae in two of the eleven subjects who showed earlylesions and in six of the seven subjects who developed atheroma plaques.These studies therefore show that the atheroma plaque is very stronglycorrelated with the presence of Chlamydia pneumoniae, but the roleplayed by the bacterium in vascular pathology is not yet defined.

The data relating to controlled clinical studies analysing the effect oftreatments in Chlamydia pneumoniae infections are limited in number.Unlike penicillin, ampicillin or the sulphamides, erythromycin,tetracycline or doxycycline show an antibiotic activity in vitro againstChlamydia pneumoniae. However, a treatment at high doses should becontinued for several weeks in order to avoid a recurrence of theinfection. Accordingly, the use of two new macrolides, clarithromycinand azithromycin, whose diffusion, bioavailability and half-life allowshorter and better tolerated cures, is nowadays preferred. In theabsence of definitive proof based on the results of clinical studies, aneffective, without recurrences, and well-tolerated treatment ofChlamydia pneumoniae infections therefore remains desirable.

An even more important need up until now relates to a specific andsensitive diagnosis, which can be carried out conveniently and rapidly,allowing early screening for the infection. Methods based on Chlamydiapneumoniae culture are slow and require a considerable know-how becauseof the difficulty involved in the collection, preservation and storageof the strain under appropriate conditions. Methods based on antigendetection (EIA, DFA) or on nucleic acid amplification (PCR) providetests which are more suitable for laboratory practice. A reliable,sensitive and convenient test, which allows distinction betweenserogroups and a fortiori between Chlamydia pneumoniae species istherefore highly desirable.

This is all the more important since the symptoms of Chlamydiapneumoniae infection appear slowly, since all the pathologies associatedwith these infections have not yet been identified, and since, as hasbeen mentioned above, an association is suspected between theseinfections and serious chronic infections, asthma or atherosclerosis.

No vaccine is yet available against Chlamydia pneumoniae: this is due tothe labile nature of the antigens specific to the strain, which has sofar prevented their specific identification.

Although the number of studies and of animal models developed is high,the antigens used have not induced sufficient protective immunity tolead to the development of human vaccines. In the case of Chlamydiapneumoniae, the role of the immune defense in the physiology andpathology of the disease should probably be understood in order todevelop satisfactory vaccines.

More detailed information relating to the biology of these strains,their interactions with their hosts, the associated phenomena ofinfectivity and those of escaping the immune defenses of the host inparticular, and finally their involvement in the development of thethese associated pathologies, will allow a better understanding of thesemechanisms. In the light of the preceding text which shows in particularthe limitations of the means of controlling Chlamydia pneumoniaeinfection, it is therefore at present essential, on the one hand, todevelop molecular tools, in particular from a better genetic knowledgeof Chlamydia pneumoniae, but also to develop new preventive andtherapeutic treatments, new diagnostic methods and new vaccinestrategies which are specific, effective and tolerated. This isprecisely the object of the present invention.

The subject of the present invention is the nucleotide sequence havingthe sequence SEQ ID No. 1 of the Chlamydia pneumoniae genome. However,the invention is not limited to SEQ ID No. 1, but encompasses genomesand nucleotides encoding polypeptides of strain variants, polymorphisms,allelic variants, and mutants.

Thus, the subject of the present invention encompasses nucleotidesequences characterized in that they are chosen from:

-   a) the nucleotide sequence of SEQ ID No. 1, a nucleotide sequence    exhibiting at least 99.9% identity with the sequence SEQ ID No. 1,    the nucleotide sequence of the genomic DNA contained within ATCC    Deposit No. VR2634, the nucleotide sequence of a clone insert within    ATCC Deposit No. 207000; 207001; and 207002;-   b) a nucleotide sequence homologous to the sequence SEQ ID No. 1;-   c) a polynucleotide sequence that hybridizes to the nucleotide    sequence of a) under conditions of high or intermediate stringency    as described below:    -   (i) By way of example and not limitation, procedures using        conditions of high stringency are as follows: Prehybridization        of filters containing DNA is carried out for 8 h to overnight at        65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1        mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml        denatured salmon sperm DNA. Filters are hybridized for 48 h at        65° C., the preferred hybridization temperature, in        prehybridization mixture containing 100 μg/ml denatured salmon        sperm DNA and 5–20×10⁶ cpm of ³²P-labeled probe. Alternatively,        the hybridization step can be performed at 65° C. in the        presence of SSC buffer, 1×SSC corresponding to 0.15M NaCl and        0.05 M Na citrate. Subsequently, filter washes can be done at        37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01%        Ficoll, and 0.01% BSA, followed by a wash in 0.1×SSC at 50° C.        for 45 min. Alternatively, filter washes can be performed in a        solution containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS,        or 0.1×SSC and 0.1% SDS at 68° C. for 15 minute intervals.        Following the wash steps, the hybridized probes are detectable        by autoradiography. Other conditions of high stringency which        may be used are well known in the art and as cited in Sambrook        et al., 1989, Molecular Cloning, A Laboratory Manual, Second        Edition, Cold Spring Harbor Press, N.Y., pp. 9.47–9.57; and        Ausubel et al., 1989, Current Protocols in Molecular Biology,        Green Publishing Associates and Wiley Interscience, N.Y. are        incorporated herein in their entirety.    -   (ii) By way of example and not limitation, procedures using        conditions of intermediate stringency are as follows: Filters        containing DNA are prehybridized, and then hybridized at a        temperature of 60° C. in the presence of a 5×SSC buffer and        labeled probe. Subsequently, filters washes are performed in a        solution containing 2×SSC at 50° C. and the hybridized probes        are detectable by autoradiography. Other conditions of        intermediate stringency which may be used are well known in the        art and as cited in Sambrook et al., 1989, Molecular Cloning, A        Laboratory Manual, Second Edition, Cold Spring Harbor Press,        N.Y., pp. 9.47–9.57; and Ausubel et al., 1989, Current Protocols        in Molecular Biology, Green Publishing Associates and Wiley        Interscience, N.Y. are incorporated herein in their entirety.-   d) a nucleotide sequence complementary to the sequence SEQ ID No. 1    or complementary to a nucleotide sequence as defined in a), b) or c)    and a nucleotide sequence of their corresponding RNA;-   e) a nucleotide sequence of a representative fragment of the    sequence SEQ ID No. 1, or of a representative fragment of the    nucleotide sequence as defined in a), b), c) or d);-   f) a nucleotide sequence comprising a sequence as defined in a), b),    c), d) or e);-   g) a nucleotide sequence capable of being obtained from a nucleotide    sequence as defined in a), b), c), d), e) or f); and-   h) a modified nucleotide sequence of a nucleotide sequence as    defined in a), b), c), d), e), f) or g).

Nucleotide sequence, polynucleotide or nucleic acid are understood tomean, according to the present invention, either a double-stranded DNA,a single-stranded DNA or products of transcription of the said DNAs.

It should be understood that the present invention does not relate tothe genomic nucleotide sequences of Chlamydia pneumoniae taken in theirnatural environment, that is to say in the natural state. They aresequences which may have been isolated, purified or partially purified,by separation methods such as, for example, ion-exchange chromatography,molecular size exclusion chromatography or affinity chromatography, oralternatively fractionation techniques based on solubility in varioussolvents, or by genetic engineering methods such as amplification,cloning or subcloning, it being possible for the sequences of theinvention to be carried by vectors.

The nucleotide sequence SEQ ID No. 1 was obtained by sequencing theChlamydia pneumoniae genome by the method of directed sequencing afterfluorescent automated sequencing of the inserts of clones and assemblingof these sequences of nucleotide fragments (inserts) by means ofsoftwares (cf. Examples). In spite of the high precision of the sequenceSEQ ID No. 1, it is possible that it does not perfectly, 100% representthe nucleotide sequence of the Chlamydia pneumoniae genome and that afew rare sequencing errors or uncertainties still remain in the sequenceSEQ ID No. 1. In the present invention, the presence of an uncertaintyfor an amino acid is designated by “Xaa” and that for a nucleotide isdesignated by “N” in the sequence listing below. These few rare errorsor uncertainties could be easily detected and corrected by personsskilled in the art using the entire chromosome and/or its representativefragments according to the invention and standard amplification, cloningand sequencing methods, it being possible for the sequences obtained tobe easily compared, in particular by means of a computer software andusing computer-readable media for recording the sequences according tothe invention as described, for example, below. After correcting thesepossible rare errors or uncertainties, the corrected nucleotide sequenceobtained would still exhibit at least 99.9% identity with the sequenceSEQ ID No. 1. Such rare sequencing uncertainties are not present withinthe DNA contained within ATCC Deposit No. VR2634; 207000; 207001; or207002, and whatever rare sequence uncertainties that exist within SEQID No. 1 can routinely be corrected utilizing the DNA of the ATCCdeposits.

Homologous nucleotide sequence for the purposes of the present inventionis understood to mean a nucleotide sequence having a percentage identitywith the bases of the nucleotide sequence SEQ ID No. 1 of at least 80%,preferably 90% and 95%, this percentage being purely statistical and itbeing possible for the differences between the two nucleotide sequencesto be distributed randomly and over their entire length. The saidhomologous sequences exhibiting a percentage identity with the bases ofthe nucleotide sequence SEQ ID No. 1 of at least 80%, preferably 90% and95%, may comprise, for example, the sequences corresponding to thegenomic sequence or to the sequences of its representative fragments ofa bacterium belonging to the Chlamydia family, including the speciesChlamydia trachomatis, Chlamydia psittaci and Chlamydia pecorummentioned above, as well as the sequences corresponding to the genomicsequence or to the sequences of its representative fragments of abacterium belonging to the variants of the species Chlamydia pneumoniae.In the present invention, the terms family and genus are mutuallyinterchangeable, the terms variant, serotype, strain and subspecies arealso mutually interchangeable. These homologous sequences may thuscorrespond to variations linked to mutations within the same species orbetween species and may correspond in particular to truncations,substitutions, deletions and/or additions of at least one nucleotide.The said homologous sequences may also correspond to variations linkedto the degeneracy of the genetic code or to a bias in the genetic codewhich is specific to the family, to the species or to the variant andwhich are likely to be present in Chlamydia.

Protein and/or nucleic acid sequence homologies may be evaluated usingany of the variety of sequence comparison algorithms and programs knownin the art. Such algorithms and programs include, but are by no meanslimited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson andLipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444–2448; Altschul etal., 1990, J. Mol. Biol. 215(3):403–410; Thompson et al., 1994, NucleicAcids Res. 22(2):4673–4680; Higgins et al., 1996, Methods Enzymol.266:383–402; Altschul et al., 1990, J. Mol. Biol. 215(3):403–410;Altschul et al., 1993, Nature Genetics 3:266–272).

In a particularly preferred embodiment, protein and nucleic acidsequence homologies are evaluated using the Basic Local Alignment SearchTool (“BLAST”) which is well known in the art (see, e.g., Karlin andAltschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267–2268; Altschul etal., 1990, J. Mol. Biol. 215:403–410; Altschul et al., 1993, NatureGenetics 3:266–272; Altschul et al., 1997, Nuc. Acids Res.25:3389–3402). In particular, five specific BLAST programs are used toperform the following task:

(1) BLASTP and BLAST3 compare an amino acid query sequence against aprotein sequence database;

(2) BLASTN compares a nucleotide query sequence against a nucleotidesequence database;

(3) BLASTX compares the six-frame conceptual translation products of aquery nucleotide sequence (both strands) against a protein sequencedatabase;

(4) TBLASTN compares a query protein sequence against a nucleotidesequence database translated in all six reading frames (both strands);and

(5) TBLASTX compares the six-frame translations of a nucleotide querysequence against the six-frame translations of a nucleotide sequencedatabase.

The BLAST programs identify homologous sequences by identifying similarsegments, which are referred to herein as “high-scoring segment pairs,”between a query amino or nucleic acid sequence and a test sequence whichis preferably obtained from a protein or nucleic acid sequence database.High-scoring segment pairs are preferably identified (i.e., aligned) bymeans of a scoring matrix, many of which are known in the art.Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet etal., 1992, Science 256:1443–1445; Henikoff and Henikoff, 1993, Proteins17:49–61). Less preferably, the PAM or PAM250 matrices may also be used(see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for DetectingDistance Relationships: Atlas of Protein Sequence and Structure,Washington: National Biomedical Research Foundation)

The BLAST programs evaluate the statistical significance of allhigh-scoring segment pairs identified, and preferably selects thosesegments which satisfy a user-specified threshold of significance, suchas a user-specified percent homology. Preferably, the statisticalsignificance of a high-scoring segment pair is evaluated using thestatistical significance formula of Karlin (see, e.g., Karlin andAltschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267–2268).

Nucleotide sequence complementary to a sequence of the invention isunderstood to mean any DNA whose nucleotides are complementary to thoseof the sequence of the invention, and whose orientation is reversed(antiparallel sequence).

The present invention further comprises fragments of the sequences of a)through f), above. Representative fragments of the sequences accordingto the invention will be understood to mean any nucleotide fragmenthaving at least 8 successive nucleotides, preferably at least 12successive nucleotides, and still more preferably at least 15 or atleast 20 successive nucleotides of the sequence from which it isderived. It is understood that such fragments refer only to portions ofSEQ ID No. 1 that are not currently listed in a publicly availabledatabase.

Among these representative fragments, those capable of hybridizing understringent conditions with a nucleotide sequence according to theinvention are preferred. Hybridization under stringent conditions meansthat the temperature and ionic strength conditions are chosen such thatthey allow hybridization to be maintained between two complementary DNAfragments.

By way of illustration, high stringency conditions for the hybridizationstep for the purposes of defining the nucleotide fragments describedabove, are advantageously the following.

The hybridization is carried out at a preferred temperature of 65° C. inthe presence of SSC buffer, 1×SSC corresponding to 0.15 M NaCl and 0.05M Na citrate. The washing steps may be, for example, the following:

-   2×SSC, 0.1% SDS at room temperature followed by three washes with    1×SSC, 0.1% SDS; 0.5×SSC, 0.1% SDS; 0.11×SSC, 0.1% SDS at 68° C. for    15 minutes.

Intermediate stringency conditions, using, for example, a temperature of60° C. in the presence of a 5×SSC buffer, or of low stringency, forexample a temperature of 50° C. in the presence of a 5×SSC buffer,respectively require a lower overall complementarity for thehybridization between the two sequences.

The stringent hybridization conditions described above for apolynucleotide of about 300 bases in size will be adapted by personsskilled in the art for larger- or smaller-sized oligonucleotides,according to the teaching of Sambrook et al., 1989.

Among the representative fragments according to the invention, thosewhich can be used as primer or probe in methods which make it possibleto obtain homologous sequences or their representative fragmentsaccording to the invention, or to reconstitute a genomic fragment foundto be incomplete in the sequence SEQ ID No. 1 or carrying an error or anuncertainty, are also preferred, these methods, such as the polymerasechain reaction (PCR), cloning and sequencing of nucleic acid being wellknown to persons skilled in the art. These homologous nucleotidesequences corresponding to mutations or to inter- or intra-speciesvariations, as well as the complete genomic sequence or one of itsrepresentative fragments capable of being reconstituted, of course formpart of the invention.

Among the said representative fragments, those which can be used asprimer or probe in methods allowing diagnosis of the presence ofChlamydia pneumoniae or one of its associated microorganisms as definedbelow are also preferred.

The representative fragments capable of modulating, regulating,inhibiting or inducing the expression of a gene of Chlamydia pneumoniaeor one of its associated microorganisms, and/or capable of modulatingthe replication cycle of Chlamydia pneumoniae or one of its associatedmicroorganisms in the host cell and/or organism, are also preferred.Replication cycle is intended to designate invasion, multiplication,intracellular localization, in particular retention in the vacuole andinhibition of the process of fusion to the lysosome, and propagation ofChlamydia pneumoniae or one of its associated microorganisms from hostcells to host cells.

Among the said representative fragments, those corresponding tonucleotide sequences corresponding to open reading frames, called ORFsequences (ORF for open reading frame), and encoding polypeptides, suchas for example, but without being limited thereto, the ORF sequenceswhich will be later described, are finally preferred.

The representative fragments according to the invention may be obtained,for example, by specific amplification, such as PCR, or after digestion,with appropriate restriction enzymes, of nucleotide sequences accordingto the invention; these methods are in particular described in themanual by Sambrook et al., 1989. The said representative fragments mayalso be obtained by chemical synthesis when they are not too large insize and according to methods well known to persons skilled in the art.For example, such fragments can be obtained by isolating fragments ofthe genomic DNA of ATCC Deposit No. VR2634 or a clone insert present atthis ATCC Deposit No. 207000; 207001; or 207002.

The representative fragments according to the invention may be used, forexample, as primer, to reconstitute some of the said representativefragments, in particular those in which a portion of the sequence islikely to be missing or imperfect, by methods well known to personsskilled in the art such as amplification, cloning or sequencingtechniques.

Modified nucleotide sequence will be understood to mean any nucleotidesequence obtained by mutagenesis according to techniques well known topersons skilled in the art, and exhibiting modifications in relation tothe normal sequences, for example mutations in the regulatory and/orpromoter sequences for the expression of a polypeptide, in particularleading to a modification of the level of expression of the saidpolypeptide or to a modulation of the replicative cycle.

Modified nucleotide sequence will also be understood to mean anynucleotide sequence encoding a modified polypeptide as defined below.

The subject of the present invention also includes Chlamydia pneumoniaenucleotide sequences characterized in that they are chosen from anucleotide sequence of an open reading frame (ORF), that is, the ORF2 toORF1297 sequences.

The ORF2 to ORF1297 nucleotide sequences are defined in Tables 1 and 2,infra, by their position on the sequence SEQ ID No. 1. For example, theORF2 sequence is defined by the nucleotide sequence between thenucleotides at position 42 and 794 on the sequence SEQ ID No. 1, endsincluded. ORF2 to ORF1297 have been identified via homology analyses aswell as via analyses of potential ORF start sites, as discussed in theexamples below. It is to be understood that each identified ORF of theinvention comprises a nucleotide sequence that spans the contiguousnucleotide sequence from the ORF stop codon immediately 3′ to the stopcodon of the preceding ORF and through the 5′ codon to the next stopcodon of SEQ ID No. 1 in-frame to the ORF nucleotide sequence. Table 2,infra, lists the beginning, end and potential start site of each of ORFs1–1297. In one embodiment, the ORF comprises the contiguous nucleotidesequence spanning from the potential ORF start site downstream (that is,3′) to the ORF stop codon (or the ORF codon immediately adjacent to andupstream of the ORF stop codon). ORF2 to ORF1297 encode the polypeptidesof SEQ ID No. 2 to SEQ ID No. 1291 and of SEQ ID No. 6844 to SEQ ID No.6849, respectively.

Upon introduction of minor frameshifts, certain individual ORFs cancomprise larger “combined” ORFs. A list of such putative “combined” ORFsis shown in Table 3, below. For example, a combined ORF can comprise ORF25, ORF 26 and ORF 27, including intervening in-frame, nucleotidesequences. The order of ORFs (5′ to 3′), within each “combined” ORF isas listed. It is to be understood that when ORF2 to ORF1297 are referredto herein, such reference is also meant to include “combined” ORFs.Polypeptide sequences encoded by such “combined” ORFs are also part ofthe present invention.

Table 1 also depicts the results of homology searches that compared thesequences of the polypeptides encoded by each of the ORFs to sequencespresent in public published databases. It is understood that thosepolypeptides listed in Table 1 as exhibiting greater than about 95%identity to a polypeptide present in a publicly disclosed database arenot considered part of the present invention; likewise in thisembodiment, those nucleotide sequences encoding such polypeptides arenot considered part of the invention. In another embodiment, it isunderstood that those polypeptides listed in Table 1 as exhibitinggreater than about 99% identity to a polypeptide present in a publiclydisclosed database are not considered part of the invention; likewise,in this embodiment, those nucleotide sequences encoding suchpolypeptides are not considered part of the invention.

The invention also relates to the nucleotide sequences characterized inthat they comprise a nucleotide sequence chosen from:

-   a) an ORF2 to ORF1297, a “combined” ORF nucleotide sequence, the    nucleotide sequence of the genomic DNA contained within ATCC Deposit    No. VR2634 or a clone insert present at this ATCC Deposit No.    207000; 207001; or according to the invention;-   b) a homologous nucleotide sequence exhibiting at least 80% identity    across an entire ORF2 to ORF1297 nucleotide sequence according to    the invention or as defined in a);-   c) a polynucleotide sequence that hybridizes to ORF2 to ORF1297    under conditions of high or intermediate stringency as described    below:    -   (i) By way of example and not limitation, procedures using        conditions of high stringency are as follows: Prehybridization        of filters containing DNA is carried out for 8 h to overnight at        65° C. in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1        mM EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml        denatured salmon sperm DNA. Filters are hybridized for 48 h at        65EC, the preferred hybridization temperature, in        prehybridization mixture containing 100 μg/ml denatured salmon        sperm DNA and 5–20×10⁶ cpm of ³²P-labeled probe. Alternatively,        the hybridization step can be performed at 65EC in the presence        of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na        citrate. Subsequently, filter washes can be done at 37EC for 1 h        in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and        0.01% BSA, followed by a wash in 0.1×SSC at 50EC for 45 min.        Alternatively, filter washes can be performed in a solution        containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or        0.1×SSC and 0.1% SDS at 68EC for 15 minute intervals. Following        the wash steps, the hybridized probes are detectable by        autoradiography. Other conditions of high stringency which may        be used are well known in the art and as cited in Sambrook et        al., 1989, Molecular Cloning, A Laboratory Manual, Second        Edition, Cold Spring Harbor Press, N.Y., pp. 9.47–9.57; and        Ausubel et al., 1989, Current Protocols in Molecular Biology,        Green Publishing Associates and Wiley Interscience, N.Y. are        incorporated herein in their entirety. Preferably, such        sequences encode a homolog of a polypeptide encoded by one of        ORF2 to ORF1297. In one embodiment, such sequences encode a        Chlamydia pneumoniae polypeptide.    -   (ii) By way of example and not limitation, procedures using        conditions of intermediate stringency are as follows: Filters        containing DNA are prehybridized, and then hybridized at a        temperature of 60EC in the presence of a 5×SSC buffer and        labeled probe. Subsequently, filters washes are performed in a        solution containing 2×SSC at 50EC and the hybridized probes are        detectable by autoradiography. Other conditions of intermediate        stringency which may be used are well known in the art and as        cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory        Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp.        9.47–9.57; and Ausubel et al., 1989, Current Protocols in        Molecular Biology, Green Publishing Associates and Wiley        Interscience, N.Y. are incorporated herein in their entirety.        Preferably, such sequences encode a homolog of a polypeptide        encoded by one of ORF2 to ORF1297. In one embodiment, such        sequences encode a Chlamydia pneumoniae polypeptide.-   d) complementary or RNA nucleotide sequence corresponding to an ORF2    to ORF1297 sequence according to the invention or as defined in    a), b) or c);-   e) a nucleotide sequence of a representative fragment of an ORF2 to    ORF1297 sequence according to the invention or of a sequence as    defined in a), b), c) or d);-   f) a nucleotide sequence capable of being obtained from an ORF2 to    ORF1297 sequence according to the invention or as defined in a), b),    c), d) or e); and-   g) a modified nucleotide sequence of an ORF2 to ORF1297 sequence    according to the invention or as defined in a), b), c), d), e) or    f).

As regards the homology with the ORF2 to ORF1297 nucleotide sequences,the homologous sequences exhibiting a percentage identity with the basesof one of the ORF2 to ORF1297 nucleotide sequences of at least 80%,preferably 90% and 95%, are preferred. Such homologous sequences areidentified routinely via, for example, the algorithms described aboveand in the examples below. The said homologous sequences correspond tothe homologous sequences as defined above and may comprise, for example,the sequences corresponding to the ORF sequences of a bacteriumbelonging to the Chlamydia family, including the species Chlamydiatrachomatis, Chlamydia psittaci and Chlamydia pecorum mentioned above,as well as the sequences corresponding to the ORF sequences of abacterium belonging to the variants of the species Chlamydia pneumoniae.These homologous sequences may likewise correspond to variations linkedto mutations within the same species or between species and maycorrespond in particular to truncations, substitutions, deletions and/oradditions of at least one nucleotide. The said homologous sequences mayalso correspond to variations linked to the degeneracy of the geneticcode or to a bias in the genetic code which is specific to the family,to the species or to the variant and which are likely to be present inChlamydia.

The invention comprises polypeptides encoded by a nucleotide sequenceaccording to the invention, preferably by a representative fragment ofthe sequence SEQ ID No. 1 and corresponding to an ORF sequence, inparticular the Chlamydia pneumoniae polypeptides, characterized in thatthey are chosen from the sequences SEQ ID No. 2 to SEQ ID No. 1291 orSEQ ID No. 6844 to SEQ ID No. 6849 and representative fragments thereof.However, the invention is not limited to polypeptides encoded by ORFs inSEQ ID No. 1 and its corresponding ORF sequences, but encompassespolypeptides of strain variants, polymorphisms, allelic variants, andmutants.

Thus, the invention also comprises the polypeptides characterized inthat they comprise a polypeptide chosen from:

-   a) a polypeptide encoded by a polynucleotide sequence in SEQ ID No.    1 (e.g., any polypeptide encoded by a polynucleotide sequence    corresponding to ORF2 to ORF1297 and/or representative fragments    thereof) according to the invention;-   b) a polypeptide homologous to a polypeptide according to the    invention, or as defined in a);-   c) a polypeptide encoded by a polynucleotide sequence that    hybridizes to SEQ ID No. 1 or ORF2 to ORF1297 under high or    intermediate stringency as described below:    -   (i) By way of example and not limitation, procedures using        conditions of high stringency are as follows: Prehybridization        of filters containing DNA is carried out for 8 h to overnight at        65EC in buffer composed of 6×SSC, 50 mM Tris-HCl (pH 7.5), 1 mM        EDTA, 0.02% PVP, 0.02% Ficoll, 0.02% BSA, and 500 μg/ml        denatured salmon sperm DNA. Filters are hybridized for 48 h at        65EC, the preferred hybridization temperature, in        prehybridization mixture containing 100 μg/ml denatured salmon        sperm DNA and 5–20×10⁶ cpm of ³²P-labeled probe. Alternatively,        the hybridization step can be performed at 65EC in the presence        of SSC buffer, 1×SSC corresponding to 0.15M NaCl and 0.05 M Na        citrate. Subsequently, filter washes can be done at 37EC for 1 h        in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll, and        0.01% BSA, followed by a wash in 0.1×SSC at 50EC for 45 min.        Alternatively, filter washes can be performed in a solution        containing 2×SSC and 0.1% SDS, or 0.5×SSC and 0.1% SDS, or        0.1×SSC and 0.1% SDS at 68EC for 15 minute intervals. Following        the wash steps, the hybridized probes are detectable by        autoradiography. Other conditions of high stringency which may        be used are well known in the art and as cited in Sambrook et        al., 1989, Molecular Cloning, A Laboratory Manual, Second        Edition, Cold Spring Harbor Press, N.Y., pp. 9.47–9.57; and        Ausubel et al., 1989, Current Protocols in Molecular Biology,        Green Publishing Associates and Wiley Interscience, N.Y. are        incorporated herein in their entirety. Preferably such        polypeptide represents a homolog of a polypeptide encoded by        ORF2 to ORF1297. Preferably, such sequences encode a homolog of        a polypeptide encoded by one of ORF2 to ORF1297. In one        embodiment, such sequences encode a Chlamydia pneumoniae        polypeptide.    -   (ii) By way of example and not limitation, procedures using        conditions of intermediate stringency are as follows: Filters        containing DNA are prehybridized, and then hybridized at a        temperature of 60EC in the presence of a 5×SSC buffer and        labeled probe. Subsequently, filters washes are performed in a        solution containing 2×SSC at 50EC and the hybridized probes are        detectable by autoradiography. Other conditions of intermediate        stringency which may be used are well known in the art and as        cited in Sambrook et al., 1989, Molecular Cloning, A Laboratory        Manual, Second Edition, Cold Spring Harbor Press, N.Y., pp.        9.47–9.57; and Ausubel et al., 1989, Current Protocols in        Molecular Biology, Green Publishing Associates and Wiley        Interscience, N.Y. are incorporated herein in their entirety.        Preferably, such sequences encode a homolog of a polypeptide        encoded by one of ORF2 to ORF1297. In one embodiment, such        sequences encode a Chlamydia pneumoniae polypeptide.-   d) a fragment of at least 5 amino acids of a polypeptide according    to the invention, or as defined in a), b) or c);-   e) a biologically active fragment of a polypeptide according to the    invention, or as defined in a), b), c) or d); and-   f) a modified polypeptide of a polypeptide according to the    invention, as defined in a), b), c), d) or e).

In the present description, the terms polypeptide, peptide and proteinare interchangeable.

It should be understood that the invention does not relate to thepolypeptides in natural form, that is to say that they are not taken intheir natural environment but that they may have been isolated orobtained by purification from natural sources, or alternatively obtainedby genetic recombination, or else by chemical synthesis and that theymay, in this case, comprise nonnatural amino acids, as will be describedbelow.

Homologous polypeptide will be understood to designate the polypeptidesexhibiting, in relation to the natural polypeptide, certainmodifications such as in particular a deletion, addition or substitutionof at least one amino acid, a truncation, an extension, a chimericfusion, and/or a mutation, or polypeptides exhibiting post-translationalmodifications. Among the homologous polypeptides, those whose amino acidsequence exhibits at least 80%, preferably 90%, homology or identitywith the amino acid sequences of the polypeptides according to theinvention are preferred. In the case of a substitution, one or moreconsecutive or nonconsecutive amino acids are replaced by “equivalent”amino acids. The expression “equivalent” amino acid is intended here todesignate any amino acid capable of being substituted for one of theamino acids in the basic structure without, however, essentiallymodifying the biological activities of the corresponding peptides and aswill be defined later.

Protein and/or nucleic acid sequence homologies may be evaluated usingany of the variety of sequence comparison algorithms and programs knownin the art. Such algorithms and programs include, but are by no meanslimited to, TBLASTN, BLASTP, FASTA, TFASTA, and CLUSTALW (Pearson andLipman, 1988, Proc. Natl. Acad. Sci. USA 85(8):2444–2448; Altschul etal., 1990, J. Mol. Biol. 215(3):403–410; Thompson et al., 1994, NucleicAcids Res. 22(2):4673–4680; Higgins et al., 1996, Methods Enzymol.266:383–402; Altschul et al., 1990, J. Mol. Biol. 215(3):403–410;Altschul et al., 1993, Nature Genetics 3:266–272).

In a particularly preferred embodiment, protein and nucleic acidsequence homologies are evaluated using the Basic Local Alignment SearchTool (“BLAST”) which is well know in the art (see, e.g., Karlin andAltschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267–2268; Altschul etal., 1990, J. Mol. Biol. 215:403–410; Altschul et al., 1993, NatureGenetics 3:266–272; Altschul et al., 1997, Nuc. Acids Res.25:3389–3402). In particular, five specific BLAST programs are used toperform the following task:

(1) BLASTP and BLAST3 compare an amino acid query sequence against aprotein sequence database;

(2) BLASTN compares a nucleotide query sequence against a nucleotidesequence database;

(3) BLASTX compares the six-frame conceptual translation products of aquery nucleotide sequence (both strands) against a protein sequencedatabase;

(4) TBLASTN compares a query protein sequence against a nucleotidesequence database translated in all six reading frames (both strands);and

(5) TBLASTX compares the six-frame translations of a nucleotide querysequence against the six-frame translations of a nucleotide sequencedatabase.

The BLAST programs identify homologous sequences by identifying similarsegments, which are referred to herein as “high-scoring segment pairs,”between a query amino or nucleic acid sequence and a test sequence whichis preferably obtained from a protein or nucleic acid sequence database.High-scoring segment pairs are preferably identified (i.e., aligned) bymeans of a scoring matrix, many of which are known in the art.Preferably, the scoring matrix used is the BLOSUM62 matrix (Gonnet etal., 1992, Science 256:1443–1445; Henikoff and Henikoff, 1993, Proteins17:49–61). Less preferably, the PAM or PAM250 matrices may also be used(see, e.g., Schwartz and Dayhoff, eds., 1978, Matrices for DetectingDistance Relationships: Atlas of Protein Sequence and Structure,Washington: National Biomedical Research Foundation)

The BLAST programs evaluate the statistical significance of allhigh-scoring segment pairs identified, and preferably selects thosesegments which satisfy a user-specified threshold of significance, suchas a user-specified percent homology. Preferably, the statisticalsignificance of a high-scoring segment pair is evaluated using thestatistical significance formula of Karlin (see, e.g., Karlin andAltschul, 1990, Proc. Natl. Acad. Sci. USA 87:2267–2268).

Equivalent amino acids may be determined either based on theirstructural homology with the amino acids for which they are substituted,or on results of comparative tests of biological activity between thevarious polypeptides which may be carried out.

By way of example, there may be mentioned the possibilities ofsubstitutions which may be carried out without resulting in asubstantial modification of the biological activity of the correspondingmodified polypeptides; the replacements, for example, of leucine withvaline or isoleucine, of aspartic acid with glutamic acid, of glutaminewith asparagine, of arginine with lysine, and the like, the reversesubstitutions naturally being feasible under the same conditions.

The homologous polypeptides also correspond to the polypeptides encodedby the homologous nucleotide sequences as defined above and thuscomprise in the present definition the mutated polypeptides orpolypeptides corresponding to inter- or intra-species variations whichmay exist in Chlamydia, and which correspond in particular totruncations, substitutions, deletions and/or additions of at least oneamino acid residue.

Biologically active fragment of a polypeptide according to the inventionwill be understood to designate in particular a polypeptide fragment, asdefined below, exhibiting at least one of the characteristics of thepolypeptides according to the invention, in particular in that it is:

-   capable of eliciting an immune response directed against Chlamydia    pneumoniae; and/or-   capable of being recognized by an antibody specific for a    polypeptide according to the invention; and/or-   capable of binding to a polypeptide or to a nucleotide sequence of    Chlamydia pneumoniae; and/or-   capable of modulating, regulating, inducing or inhibiting the    expression of a gene of Chlamydia pneumoniae or one of its    associated microorganisms, and/or capable of modulating the    replication cycle of Chlamydia pneumoniae or one of its associated    microorganisms in the host cell and/or organism; and/or-   capable of generally exerting an even partial physiological    activity, such as for example a structural activity (cellular    envelope, ribosome), an enzymatic (metabolic) activity, a transport    activity, an activity in the secretion or in the virulence.

A polypeptide fragment according to the invention is understood todesignate a polypeptide comprising a minimum of 5 amino acids,preferably 10 amino acids or preferably 15 amino acids. It is to beunderstood that such fragments refer only to portions of polypeptidesencoded by ORF2 to ORF1297 that are not currently listed in a publiclyavailable database.

The polypeptide fragments according to the invention may correspond toisolated or purified fragments which are naturally present in Chlamydiapneumoniae or which are secreted by Chlamydia pneumoniae, or maycorrespond to fragments capable of being obtained by cleaving the saidpolypeptide with a proteolytic enzyme, such as trypsin or chymotrypsinor collagenase, or with a chemical reagent, such as cyanogen bromide(CNBr) or alternatively by placing the said polypeptide in a highlyacidic environment, for example at pH 2.5. Such polypeptide fragmentsmay be equally well prepared by chemical synthesis, using hoststransformed with an expression vector according to the inventioncontaining a nucleic acid allowing the expression of the said fragments,placed under the control of appropriate elements for regulation and/orexpression.

“Modified polypeptide” of a polypeptide according to the invention isunderstood to designate a polypeptide obtained by genetic recombinationor by chemical synthesis as will be described below, exhibiting at leastone modification in relation to the normal sequence. These modificationsmay in particular affect amino acids responsible for a specificity orfor the efficiency of the activity, or responsible for the structuralconformation, for the charge or for the hydrophobicity, and for thecapacity for multimerization and for membrane insertion of thepolypeptide according to the invention. It is thus possible to createpolypeptides with an equivalent, an increased or a reduced activity, andwith an equivalent, a narrower or a broader specificity. Among themodified polypeptides, there may be mentioned the polypeptides in whichup to 5 amino acids may be modified, truncated at the N- or C-terminalend, or alternatively deleted, or else added.

As is indicated, the modifications of the polypeptide may have inparticular the objective:

-   of making it capable of modulating, regulating, inhibiting or    inducing the expression of a gene of Chlamydia, in particular of    Chlamydia pneumoniae and its variants, or one of its associated    microorganisms, and/or capable of modulating the replication cycle    of Chlamydia, in particular of Chlamydia pneumoniae and its    variants, or one of its associated microorganisms, in the host cell    and/or organism,-   of allowing its use in methods of biosynthesis or of biodegradation,    or its incorporation into vaccine compositions,-   of modifying its bioavailability as a compound for therapeutic use.

The said modified polypeptides may also be used on any cell ormicroorganism for which the said modified polypeptides will be capableof modulating, regulating, inhibiting or inducing gene expression, or ofmodulating the growth or the replication cycle of the said cell or ofthe said microorganism. The methods allowing demonstration of the saidmodulations on eukaryotic or prokaryotic cells are well known to personsskilled in the art. The said cells or microorganisms will be chosen, inparticular, from tumour cells or infectious microorganisms and the saidmodified polypeptides may be used for the prevention or treatment ofpathologies linked to the presence of the said cells or of the saidmicroorganisms. It is also clearly understood that the nucleotidesequences encoding the said modified polypeptides may be used for thesaid modulations, for example by the intermediacy of vectors accordingto the invention and which are described below, so as to prevent or totreat the said pathologies.

The above modified polypeptides may be obtained using combinatorychemistry, in which it is possible to systematically vary portions ofthe polypeptide before testing them on models, cell cultures ormicroorganisms for example, so as to select the compounds which are themost active or which exhibit the desired properties.

Chemical synthesis also has the advantage of being able to use:

-   -   nonnatural amino acids, or    -   nonpeptide bonds.

Accordingly, in order to extend the life of the polypeptides accordingto the invention, it may be advantageous to use nonnatural amino acids,for example in the D form, or alternatively amino acid analogues, inparticular sulphur-containing forms for example.

Finally, the structure of the polypeptides according to the invention,its homologous or modified forms, as well as the corresponding fragmentsmay be integrated into chemical structures of the polypeptide type andthe like. Accordingly, it may be advantageous to provide at the N- andC-terminal ends compounds which are not recognized by proteases.

Also forming part of the invention are the nucleotide sequences encodinga polypeptide according to the invention. Described below are ORFnucleotide sequences encoding polypeptides exhibiting particularlypreferable characteristics. For each group of preferred ORFS describedbelow, it is to be understood that in addition to the individual ORFslisted, in instances wherein such ORFS are present as part of “combined”ORFs, the “combined” ORFs are also to be included within the preferredgroup.

More particularly, the subject of the invention is nucleotide sequences,characterized in that they encode a polypeptide of the cellularenvelope, preferably of the outer cellular envelope of Chlamydiapneumoniae or one of its representative fragments, such as for examplethe predominant proteins of the outer membrane, the adhesion proteins orthe proteins entering into the composition of the Chlamydia wall. Amongthese sequences, the sequences comprising a nucleotide sequence chosenfrom the following sequences are most preferred:

ORF15; ORF25; ORF26; ORF27; ORF28; ORF29; ORF30; ORF31; ORF32; ORF33;ORF35; ORF68; ORF124; ORF275; ORF291; ORF294; ORF327; ORF342; ORF364;ORF374; ORF380; ORF414; ORF439; ORF466; ORF467; ORF468; ORF469; ORF470;ORF472; ORF474; ORF476; ORF477; ORF478; ORF479; ORF480; ORF482; ORF485;ORF500; ORF501; ORF503; ORF504; ORF505; ORF506; ORF520; ORF578; ORF580;ORF581; ORF595; ORF596; ORF597; ORF737; ORF830; ORF834; ORF836; ORF893;ORF917; ORF932; ORF976; ORF1035; ORF1045; ORF1090 and one of theirrepresentative fragments.

The structure of the cytoplasmic membranes and of the wall of bacteriais dependent on the associated proteins. The structure of thecytoplasmic membrane makes it impermeable to water, to water-solublesubstances and to small-sized molecules (ions, small inorganicmolecules, peptides or proteins). To enter into or to interfere with acell or a bacterium, a ligand must establish a special relationship witha protein anchored in the cytoplasmic membrane (the receptor). Theseproteins which are anchored on the membrane play an important role inmetabolism since they control the exchanges in the bacterium. Theseexchanges apply to molecules of interest for the bacterium (smallmolecules such as sugars and small peptides) as well as undesirablemolecules for the bacterium such as antibiotics or heavy metals.

The double lipid layer structure of the membrane requires the proteinswhich are inserted therein to have hydrophobic domains of about twentyamino acids forming an alpha helix. Predominantly hydrophobic andpotentially transmembrane regions may be predicted from the primarysequence of the proteins, itself deduced from the nucleotide sequence.The presence of one or more putative transmembrane domains raises thepossibility for a protein to be associated with the cytoplasmic membraneand to be able to play an important metabolic role therein oralternatively for the protein thus exposed to be able to exhibitpotentially protective epitopes.

If the proteins inserted into the membrane exhibit several transmembranedomains capable of interacting with one another via electrostatic bonds,it then becomes possible for these proteins to form pores which goacross the membrane which becomes permeable for a number of substances.It should be noted that proteins which do not have transmembrane domainsmay also be anchored by the intermediacy of fatty acids in thecytoplasmic membrane, it being possible for the breaking of the bondbetween the protein and its anchor in some cases to be responsible forthe release of the peptide outside the bacterium.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae transmembrane polypeptide or one of its representativefragments, having between 1 and 3 transmembrane domains and in that theycomprise a nucleotide sequence chosen from the following sequences:

ORF2; ORF3; ORF6; ORF9; ORF10; ORF11; ORF13; ORF14; ORF16; ORF18; ORF19;ORF20; ORF21; ORF22; ORF25; ORF27; ORF28; ORF29; ORF30; ORF31; ORF32;ORF33; ORF34; ORF35; ORF37; ORF39; ORF41; ORF42; ORF44; ORF45; ORF46;ORF47; ORF48; ORF49; ORF50; ORF53; ORF54; ORF56; ORF57; ORF59; ORF60;ORF61; ORF62; ORF63; ORF64; ORF65; ORF66; ORF69; ORF72; ORF73; ORF74;ORF76; ORF77; ORF78; ORF79; ORF80; ORF82; ORF84; ORF85; ORF86; ORF88;ORF89; ORF90; ORF91; ORF92; ORF93; ORF95; ORF96; ORF98; ORF99; ORF100;ORF101; ORF102; ORF103; ORF104; ORF105; ORF106; ORF107; ORF108; ORF114;ORF117; ORF118; ORF122; ORF123; ORF124; ORF125; ORF129; ORF130; ORF131;ORF132; ORF133; ORF134; ORF135; ORF137; ORF138; ORF139; ORF140; ORF141;ORF142; ORF143; ORF145; ORF146; ORF147; ORF150; ORF151; ORF152; ORF156;ORF157; ORF158; ORF159; ORF160; ORF161; ORF162; ORF164; ORF166; ORF167;ORF170; ORF173; ORF175; ORF176; ORF178; ORF179; ORF180; ORF182; ORF183;ORF184; ORF185; ORF186; ORF187; ORF188; ORF189; ORF190; ORF191; ORF192;ORF194; ORF195; ORF196; ORF197; ORF198; ORF199; ORF200; ORF201; ORF202;ORF205; ORF207; ORF208; ORF209; ORF210; ORF212; ORF215; ORF219; ORF220;ORF224; ORF226; ORF227; ORF228; ORF231; ORF232; ORF233; ORF234; ORF235;ORF236; ORF238; ORF239; ORF240; ORF241; ORF242; ORF244; ORF247; ORF251;ORF252; ORF253; ORF255; ORF256; ORF257; ORF258; ORF260; ORF262; ORF263;ORF266; ORF267; ORF268; ORF269; ORF270; ORF273; ORF274; ORF276; ORF278;ORF279; ORF280; ORF281; ORF282; ORF283; ORF284; ORF286; ORF287; ORF289;ORF290; ORF291; ORF293; ORF294; ORF297; ORF304; ORF305; ORF307; ORF308;ORF309; ORF310; ORF311; ORF313; ORF314; ORF315; ORF316; ORF318; ORF319;ORF320; ORF321; ORF322; ORF323; ORF324; ORF325; ORF326; ORF331; ORF332;ORF336; ORF338; ORF339; ORF341; ORF344; ORF345; ORF346; ORF350; ORF352;ORF353; ORF356; ORF357; ORF358; ORF359; ORF360; ORF362; ORF365; ORF366;ORF367; ORF370; ORF372; ORF373; ORF376; ORF377; ORF378; ORF379; ORF381;ORF382; ORF383; ORF384; ORF385; ORF386; ORF387; ORF390; ORF392; ORF393;ORF394; ORF396; ORF398; ORF399; ORF400; ORF404; ORF408; ORF410; ORF411;ORF413; ORF416; ORF417; ORF418; ORF420; ORF422; ORF424; ORF427; ORF428;ORF429; ORF430; ORF431; ORF433; ORF434; ORF437; ORF440; ORF441; ORF442;ORF443; ORF444; ORF445; ORF447; ORF450; ORF451; ORF452; ORF455; ORF456;ORF459; ORF460; ORF461; ORF462; ORF463; ORF464; ORF465; ORF467; ORF469;ORF471; ORF474; ORF475; ORF476; ORF477; ORF479; ORF482; ORF483; ORF484;ORF485; ORF486; ORF487; ORF488; ORF491; ORF493; ORF494; ORF497; ORF498;ORF499; ORF503; ORF508; ORF509; ORF510; ORF512; ORF514; ORF515; ORF516;ORF517; ORF518; ORF520; ORF521; ORF523; ORF525; ORF527; ORF528; ORF529;ORF530; ORF531; ORF533; ORF534; ORF535; ORF536; ORF537; ORF540; ORF541;ORF543; ORF544; ORF545; ORF546; ORF548; ORF549; ORF551; ORF553; ORF554;ORF555; ORF556; ORF557; ORF558; ORF559; ORF560; ORF562; ORF563; ORF564;ORF565; ORF566; ORF569; ORF571; ORF573; ORF576; ORF577; ORF581; ORF583;ORF584; ORF585; ORF586; ORF588; ORF591; ORF592; ORF594; ORF595; ORF596;ORF597; ORF599; ORF600; ORF603; ORF605; ORF608; ORF614; ORF615; ORF620;ORF621; ORF622; ORF623; ORF624; ORF625; ORF629; ORF630; ORF631; ORF633;ORF634; ORF637; ORF642; ORF644; ORF645; ORF647; ORF648; ORF652; ORF654;ORF655; ORF657; ORF658; ORF659; ORF660; ORF661; ORF664; ORF665; ORF666;ORF667; ORF670; ORF671; ORF672; ORF673; ORF674; ORF676; ORF679; ORF681;ORF684; ORF687; ORF688; ORF689; ORF690; ORF693; ORF694; ORF695; ORF696;ORF697; ORF698; ORF699; ORF700; ORF701; ORF703; ORF705; ORF706; ORF707;ORF708; ORF710; ORF712; ORF715; ORF716; ORF717; ORF718; ORF719; ORF721;ORF722; ORF723; ORF725; ORF726; ORF727; ORF728; ORF729; ORF730; ORF731;ORF733; ORF736; ORF737; ORF738; ORF740; ORF741; ORF742; ORF743; ORF747;ORF748; ORF750; ORF752; ORF754; ORF755; ORF756; ORF757; ORF759; ORF760;ORF761; ORF762; ORF763; ORF764; ORF765; ORF766; ORF767; ORF768; ORF772;ORF774; ORF775; ORF777; ORF781; ORF783; ORF788; ORF791; ORF792; ORF793;ORF794; ORF795; ORF796; ORF797; ORF798; ORF799; ORF802; ORF803; ORF806;ORF807; ORF808; ORF809; ORF810; ORF811; ORF813; ORF814; ORF815; ORF816;ORF817; ORF819; ORF820; ORF821; ORF823; ORF824; ORF827; ORF829; ORF830;ORF831; ORF833; ORF834; ORF835; ORF837; ORF844; ORF845; ORF846; ORF847;ORF848; ORF849; ORF850; ORF851; ORF852; ORF854; ORF855; ORF856; ORF857;ORF859; ORF860; ORF862; ORF865; ORF866; ORF868; ORF869; ORF870; ORF871;ORF872; ORF874; ORF877; ORF878; ORF879; ORF880; ORF881; ORF882; ORF884;ORF885; ORF888; ORF889; ORF890; ORF891; ORF892; ORF894; ORF895; ORF896;ORF897; ORF899; ORF900; ORF902; ORF903; ORF904; ORF905; ORF909; ORF910;ORF912; ORF913; ORF914; ORF915; ORF917; ORF918; ORF919; ORF921; ORF923;ORF924; ORF926; ORF927; ORF928; ORF929; ORF930; ORF931; ORF937; ORF938;ORF939; ORF941; ORF943; ORF948; ORF951; ORF952; ORF953; ORF958; ORF960;ORF963; ORF964; ORF965; ORF968; ORF970; ORF974; ORF975; ORF977; ORF979;ORF980; ORF981; ORF983; ORF984; ORF985; ORF987; ORF989; ORF992; ORF993;ORF997; ORF998; ORF999; ORF1001; ORF1002; ORF1004; ORF1005; ORF1009;ORF1013; ORF1014; ORF1015; ORF1016; ORF1019; ORF1021; ORF1023; ORF1024;ORF1029; ORF1031; ORF1033; ORF1034; ORF1039; ORF1041; ORF1042; ORF1045;ORF1047; ORF1049; ORF1051; ORF1052; ORF1053; ORF1054; ORF1056; ORF1059;ORF1061; ORF1062; ORF1063; ORF1064; ORF1065; ORF1067; ORF1075; ORF1077;ORF1078; ORF1079; ORF1080; ORF1081; ORF1089; ORF1095; ORF1097; ORF1098;ORF1099; ORF1101; ORF1102; ORF1103; ORF1106; ORF1107; ORF1108; ORF1109;ORF1110; ORF1113; ORF1116; ORF1118; ORF1119; ORF1121; ORF1123; ORF1124;ORF1126; ORF1128; ORF1130; ORF1131; ORF1133; ORF1134; ORF1136; ORF 1137and one of their representative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae transmembrane polypeptide or one of its representativefragments, having between 4 and 6 transmembrane domains and in that theycomprise a nucleotide sequence chosen from the following sequences:

ORF5; ORF7; ORF8; ORF15; ORF36; ORF38; ORF51; ORF55; ORF58; ORF67;ORF70; ORF81; ORF97; ORF110; ORF111; ORF115; ORF119; ORF126; ORF128;ORF148; ORF155; ORF163; ORF165; ORF168; ORF169; ORF171; ORF172; ORF174;ORF177; ORF181; ORF193; ORF203; ORF213; ORF214; ORF216; ORF217; ORF221;ORF222; ORF225; ORF229; ORF243; ORF246; ORF248; ORF254; ORF261; ORF285;ORF288; ORF292; ORF296; ORF298; ORF299; ORF301; ORF303; ORF317; ORF328;ORF329; ORF351; ORF354; ORF355; ORF364; ORF371; ORF374; ORF375; ORF391;ORF395; ORF401; ORF403; ORF405; ORF409; ORF414; ORF419; ORF421; ORF423;ORF425; ORF438; ORF448; ORF453; ORF458; ORF466; ORF468; ORF470; ORF480;ORF489; ORF490; ORF496; ORF501; ORF504; ORF505; ORF506; ORF511; ORF513;ORF519; ORF526; ORF532; ORF538; ORF539; ORF547; ORF550; ORF561; ORF568;ORF570; ORF574; ORF578; ORF579; ORF580; ORF582; ORF589; ORF593; ORF598;ORF601; ORF604; ORF610; ORF613; ORF617; ORF626; ORF632; ORF635; ORF638;ORF640; ORF641; ORF646; ORF649; ORF650; ORF651; ORF686; ORF711; ORF724;ORF732; ORF734; ORF744; ORF745; ORF749; ORF751; ORF769; ORF770; ORF771;ORF773; ORF776; ORF779; ORF780; ORF785; ORF787; ORF789; ORF801; ORF805;ORF812; ORF822; ORF825; ORF826; ORF839; ORF841; ORF843; ORF853;:ORF861;ORF875; ORF876; ORF886; ORF893; ORF898; ORF906; ORF907; ORF908; ORF920;ORF922; ORF925; ORF933; ORF935; ORF936; ORF944; ORF946; ORF947; ORF954;ORF959; ORF961; ORF966; ORF967; ORF972; ORF978; ORF995; ORF996; ORF1000;ORF1003; ORF1010; ORF1011; ORF1012; ORF1017; ORF1020; ORF1030; ORF1036;ORF1038; ORF1043; ORF1046; ORF1048; ORF1050; ORF1058; ORF1071; ORF1073;ORF1084; ORF1085; ORF1086; ORF1087; ORF1091; ORF1092; ORF1094; ORF1096;ORF1100; ORF1104; ORF1111; ORF1112; ORF1114; ORF1117; ORF1122; ORF1125and one of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae transmembrane polypeptide or one of itsrepresentative fragments, having at least 7 transmembrane domains and inthat they comprise a nucleotide sequence chosen from the followingsequences:

ORF17; ORF52; ORF68; ORF83; ORF87; ORF109; ORF112; ORF113; ORF120;ORF121; ORF127; ORF153; ORF204; ORF211; ORF218; ORF223; ORF275; ORF277;ORF295; ORF300; ORF302; ORF306; ORF327; ORF335; ORF342; ORF343; ORF347;ORF349; ORF361; ORF363; ORF369; ORF380; ORF388; ORF389; ORF397; ORF415;ORF432; ORF439; ORF446; ORF449; ORF472; ORF478; ORF500; ORF522; ORF524;ORF567; ORF575; ORF602; ORF606; ORF609; ORF636; ORF639; ORF643; ORF653;ORF668; ORF692; ORF702; ORF704; ORF713; ORF720; ORF778; ORF784; ORF800;ORF836; ORF838; ORF842; ORF864; ORF867; ORF883; ORF901; ORF916; ORF932;ORF934; ORF940; ORF942; ORF950; ORF956; ORF971; ORF973; ORF976; ORF988;ORF994; ORF1018; ORF1028; ORF1035; ORF1037; ORF1044; ORF1055; ORF1057;ORF1068; ORF1069; ORF1070; ORF1072; ORF1082; ORF1088; ORF1105; ORF1132;ORF1135 and one of their representative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae surface exposed polypeptide (e.g., an outer membrane protein)or one of its representative fragments, said nucleotide sequencescomprising a nucleotide sequence chosen from the following sequences:

ORF 15, ORF 25, ORF 26, ORF 27, ORF 28, ORF 29, ORF 30, ORF 31, ORF 32,ORF 33, ORF 35, ORF 36, ORF 1257, ORF 280, ORF 291, ORF 314, ORF 354,ORF 380, ORF 1266, ORF 466, ORF 467, ORF 468, ORF 469, ORF 470, ORF 472,ORF 474, ORF 476, ORF 477, ORF 478, ORF 479, ORF 480, ORF 482, ORF 483,ORF 485, ORF 486, ORF 500, ORF 501, ORF 503, ORF 504, ORF 505, ORF 506,ORF 507, ORF 1268, ORF 1269, ORF 543, ORF 544, ORF 578, ORF 579, ORF580, ORF 581, ORF 595, ORF 596, ORF 597, ORF 1271, ORF 633, ORF 637, ORF699, ORF 706, ORF 737, ORF 744, ORF 1273, ORF 751, ORF 775, ORF 776, ORF777, ORF 793, ORF 815, ORF 830, ORF 1221, ORF 849, ORF 851, ORF 852, ORF874, ORF 891, ORF 922, ORF 940, ORF 1231, ORF 1281, ORF 1035, ORF 1079,ORF 1087, ORF 1108, and one of their representative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae lipoprotein or one of its representative fragments, saidnucleotide sequences comprising a nucleotide sequence chosen from thefollowing sequences:

ORF 3, ORF 10, ORF 11, ORF 16, ORF 1254, ORF 1255, ORF 38, ORF 1256, ORF62, ORF 85, ORF 1258, ORF 115, ORF 1151, ORF 151, ORF 1259, ORF 173, ORF1261, ORF 186, ORF 194, ORF 205, ORF 214, ORF 216, ORF 217, ORF 238, ORF1177, ORF 280, ORF 291, ORF 317, ORF 327, ORF 354, ORF 364, ORF 367, ORF414, ORF 432, ORF 1192, ORF 460, ORF 1267, ORF 1268, ORF 520, ORF 536,ORF 1270, ORF 576, ORF 597, ORF 603, ORF 609, ORF 637, ORF 1272, ORF652, ORF 1213, ORF 699, ORF 705, ORF 706, ORF 708, ORF 711, ORF 727, ORF1274, ORF 800, ORF 814, ORF 825, ORF 829, ORF 830, ORF 831, ORF 844, ORF849, ORF 1275, ORF 1276, ORF 1277, ORF 872, ORF 878, ORF 880, ORF 891,ORF 892, ORF 1278, ORF 1279, ORF 1280, ORF 941, ORF 942, ORF 1282, ORF1283, ORF 952, ORF 988, ORF 998, ORF 1009, ORF 1285, ORF 1235, ORF 1028,ORF 1056, ORF 1070, ORF 1287, ORF 1087, ORF 1288, ORF 1289, ORF 1098,ORF 1246, ORF 1291, ORF 1108, ORF 1109, ORF 1112, ORF 1133, and one oftheir representative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae polypeptide involved in lipopolysaccharide (LPS)biosynthesis, said nucleotide sequences comprising a nucleotide sequencechosen from the following sequences: ORF 316, ORF 564, ORF 610, ORF 647,ORF 1211, ORF 688, ORF 924, and one of their representative fragments.

Preferably the invention relates to additional LPS-related nucleotidesequences according to the invention, characterized in that they encode:

(a) a Chlamydia pneumoniae KDO (3-deoxy-D-manno-octulosonicacid)-related polypeptide or one of its representative fragments, saidnucleotide sequences comprising a nucleotide sequence chosen from thefollowing sequences: ORF 177, ORF 1156, ORF 245, ORF 767, and one oftheir representative fragments;

(b) a Chlamydia pneumoniae phosphomannomutase-related polypeptide or oneof its representative fragments, said nucleotide sequences comprising anucleotide sequence chosen from the following sequences: ORF 74, and oneof its representative fragments;

(c) a Chlamydia pneumoniae phosphoglucomutase-related polypeptide or oneof its representative fragments, said nucleotide sequences comprising anucleotide sequence chosen from the following sequences: ORF 1286, ORF1039, and one of their representative fragments; and

(d) a Chlamydia pneumoniae lipid A component-related polypeptide or oneof its representative fragments, said nucleotide sequences comprising anucleotide sequence chosen from the following sequences: ORF 689, ORF690, ORF 691, ORF 1037, and one of their representative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae polypeptide containing RGD (Arg-Gly-Asp) attachment sites orone of its representative fragments.

-   (a) RGD-containing proteins that are outer membrane proteins, are    more likely to play a role in cell attachment. ORFs that encoded a    protein containing an RGD sequence and also were classified as outer    membrane proteins are ORF 468 and its representative fragments.-   An RGD-encoding ORF that showed homology to cds1, cds2, and copN    type III virulence loci in Chlamydia psittaci (Hsia, R. et al.    (1997), Type III secretion genes identity a putative virulence locus    of Chlamydia. Molecular Microbiology 25:351–359) is ORF 350, and its    representative fragments.-   (c) The outer membrane of Chlamydia is made of cysteine-rich    proteins that form a network of both intra and inter molecular    disulfide links. This contributes to the integrity of the membrane    since Chlamydia lacks the peptidoglycan layer that other    gram-negative bacteria have. Cysteine-rich proteins that have the    RGD sequence are also considered to be potential vaccine candidates.    Cysteine-rich proteins were defined as proteins that had more than    3.0% cysteine in their primary amino acid sequence, above the mean    genomic ORF cysteine content. The corresponding ORFs are: ORF 1290,    ORF 1294, ORF 1296, and one of their representative fragments.-   (d) The outer membrane of Chlamydia may also contain small proteins    that have cysteines in their N- and C-terminus that may contribute    to the network formed by disulfide linkages. These proteins may be    anchored in the outer membrane via their N-terminus and may have    their C-terminus exposed, which then can interact with the host    cells. Alternatively, these proteins may be anchored in the outer    membrane via both N- and C-terminus and may have regions in the    middle that may be exposed which can in turn interact with the host    cells. ORFs encoding polypeptides that contain cysteines in their    first 30 amino acids and also contain an RGD sequence are:    -   ORF 105, ORF 106, ORF 114, ORF 170, ORF 171, ORF 1264, ORF 268,        ORF 1265, ORF 350, ORF 393, ORF 394, ORF 451, ORF 452, ORF 453,        ORF 473, ORF 499, ORF 515, ORF 519, ORF 525, ORF 526, ORF 538,        ORF 611, ORF 645, ORF 686, ORF 700, ORF 746, ORF 755, ORF 756,        ORF 757, ORF 789, ORF 814, ORF 855, ORF 856, ORF 878, ORF 957,        ORF 958, ORF 989, ORF 1290, and one of their representative        fragments.-   (e) RGD-containing ORFs homologous to RGD-containing ORFs from    Chlamydia trachomatis are:    ORF 114, ORF 468, ORF 755, ORF 756, ORF 757, ORF 855, ORF 856, ORF    905, ORF 913, ORF 914, ORF 915, and one of their representative    fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae Type III or other, non-type III secreted polypeptide or oneof its representative fragments, said nucleotide sequences comprising anucleotide sequence chosen from the following sequences:

ORF 25, ORF 28, ORF 29, ORF 33, ORF 308, ORF 309, ORF 343, ORF 344, ORF345, ORF 367, ORF 414, ORF 415, ORF 480, ORF 550, ORF 579, ORF 580, ORF581, ORF 597, ORF 699, ORF 744, ORF 751, ORF 776, ORF 866, ORF 874, ORF883, ORF 884, ORF 888, ORF 891, ORF 1293, and one of theirrepresentative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode a Chlamydiapneumoniae cell wall anchored surface polypeptide or one of itsrepresentative fragments, said nucleotide sequences comprising anucleotide sequence chosen from the following sequences: ORF 267, ORF271, ORF 419, ORF 590, ORF 932, ORF 1292, ORF 1295, and one of theirrepresentative fragments.

Preferably, the invention relates to the nucleotide sequences accordingto the invention, characterized in that they encode Chlamydia pneumoniaepolypeptides not found in Chlamydia trachomatis (Blastp. P>e⁻¹⁰), saidnucleotide sequences comprising a nucleotide sequence chosen from thefollowing sequences: ORF 7, ORF 8, ORF 9, ORF 16, ORF 17, ORF 18, ORF19, ORF 20, ORF 21, ORF 22, ORF 1254, ORF 23, ORF 1255, ORF 24, ORF1139, ORF 1140, ORF 46, ORF 47, ORF 51, ORF 60, ORF 1256, ORF 61, ORF62, ORF 63, ORF 64, ORF 1257, ORF 65, ORF 66, ORF 67, ORF 68, ORF 1143,ORF 1145, ORF 83, ORF 84, ORF 1146, ORF 85, ORF 86, ORF 87, ORF 1258,ORF 116, ORF 117, ORF 125, ORF 1148, ORF 143, ORF 1150, ORF 1151, ORF144, ORF 145, ORF 147, ORF 148, ORF 149, ORF 150, ORF 152, ORF 1259, ORF162, ORF 166, ORF 1154, ORF 167, ORF 1261, ORF 1156, ORF 1157, ORF 178,ORF 179, ORF 1158, ORF 182, ORF 183, ORF 184, ORF 185, ORF 1159, ORF186, ORF 1160, ORF 187, ORF 188, ORF 189, ORF 190, ORF 1161, ORF 1162,ORF 191, ORF 192, ORF 194, ORF 195, ORF 1163, ORF 196, ORF 201, ORF 202,ORF 209, ORF 212, ORF 221, ORF 224, ORF 1167, ORF 226, ORF 227, ORF 228,ORF 229, ORF 230, ORF 231, ORF 232, ORF 1169, ORF 1170, ORF 1171, ORF234, ORF 235, ORF 236, ORF 1172, ORF 243, ORF 251, ORF 252, ORF 1176,ORF 253, ORF 255, ORF 254, ORF 256, ORF 1177, ORF 1178, ORF 262, ORF263, ORF 1264, ORF 278, ORF 279, ORF 1180, ORF 280, ORF 290, ORF 291,ORF 292, ORF 296, ORF 1181, ORF 297, ORF 298, ORF 300, ORF 1265, ORF322, ORF 324, ORF 325, ORF 370, ORF 1186, ORF 371, ORF 372, ORF 1187,ORF 373, ORF 378, ORF 1266, ORF 382, ORF 383, ORF 384, ORF 385, ORF 386,ORF 1188, ORF 1189, ORF 391, ORF 392, ORF 398, ORF 400, ORF 403, ORF1191, ORF 423, ORF 435, ORF 445, ORF 450, ORF 1193, ORF 456, ORF 460,ORF 461, ORF 465, ORF 1196, ORF 471, ORF 473, ORF 475, ORF 481, ORF 484,ORF 487, ORF 488, ORF 489, ORF 490, ORF 491, ORF 492, ORF 493, ORF 494,ORF 495, ORF 496, ORF 497, ORF 498, ORF 499, ORF 502, ORF 1267, ORF1268, ORF 508, ORF 510, ORF 509, ORF 512, ORF 515, ORF 519, ORF 1197,ORF 521, ORF 1198, ORF 522, ORF 524, ORF 528, ORF 534, ORF 537, ORF1269, ORF 1270, ORF 548, ORF 551, ORF 557, ORF 1201, ORF 1203, ORF 562,ORF 566, ORF 593, ORF 595, ORF 600, ORF 1271, ORF 604, ORF 611, ORF 612,ORF 614, ORF 616, ORF 625, ORF 627, ORF 628, ORF 629, ORF 631, ORF 641,ORF 1272, ORF 648, ORF 1212, ORF 663, ORF 685, ORF 707, ORF 714, ORF715, ORF 716, ORF 717, ORF 722, ORF 746, ORF 1273, ORF 761, ORF 764, ORF770, ORF 1217, ORF 783, ORF 1274, ORF 803, ORF 815, ORF 1220, ORF 835,ORF 1221, ORF 844, ORF 845, ORF 846, ORF 847, ORF 848, ORF 849, ORF 850,ORF 851, ORF 1275, ORF 852, ORF 862, ORF 1276, ORF 1277, ORF 873, ORF1223, ORF 892, ORF 919, ORF 1225, ORF 1278, ORF 926, ORF 1228, ORF 1229,ORF 1230, ORF 1279, ORF 1281, ORF 1282, ORF 1283, ORF 948, ORF 950, ORF949, ORF 951, ORF 980, ORF 982, ORF 1233, ORF 999, ORF 1000, ORF 1001,ORF 1002, ORF 1008, ORF 1285, ORF 1235, ORF 1016, ORF 1019, ORF 1027,ORF 1036, ORF 1241, ORF 1048, ORF 1049, ORF 1050, ORF 1053, ORF 1054,ORF 1064, ORF 1076, ORF 1091, ORF 1288, ORF 1093, ORF 1289, ORF 1101,ORF 1103, ORF 1245, ORF 1246, ORF 1247, ORF 1290, ORF 1291, ORF 1115,ORF 1116, ORF 1118, ORF 1120, ORF 1249, ORF 1121, ORF 1250, ORF 1126,ORF 1125, ORF 1127, ORF 1128, ORF 1130, ORF 1129, ORF 1131, ORF 1136,ORF 1253, ORF 1292, ORF 1294, ORF 1295, ORF 1296, and one of theirrepresentative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the intermediate metabolism, in particular in themetabolism of sugars and/or of cofactors, such as for example triosephosphate isomerase or pyruvate kinase, and in that they comprise anucleotide sequence chosen from the following sequences:

ORF2; ORF55; ORF56; ORF69; ORF75; ORF80; ORF100; ORF110; ORF114; ORF120;ORF121; ORF157; ORF160; ORF161; ORF172; ORF180; ORF181; ORF198; ORF200;ORF225; ORF248; ORF249; ORF276; ORF277; ORF318; ORF319; ORF320; ORF323;ORF331; ORF347; ORF375; ORF376; ORF381; ORF393; ORF394; ORF395; ORF396;ORF409; ORF446; ORF447; ORF448; ORF449; ORF513; ORF516; ORF571; ORF647;ORF662; ORF697; ORF718; ORF793; ORF794; ORF808; ORF809; ORF838; ORF839;ORF840; ORF853; ORF854; ORF918; ORF923; ORF929; ORF931; ORF938; ORF939;ORF958; ORF959; ORF960; ORF966; ORF995; ORF1021; ORF1040; ORF1041;ORF1042; ORF1085; ORF1100; ORF1102; ORF1117; ORF1118; ORF1119; ORF1120;ORF1135 and one of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the intermediate metabolism of nucleotides ornucleic acids, such as for example CTP synthetase or GMP synthetase, andin that they comprise a nucleotide sequence chosen from the followingsequences:

ORF77; ORF78; ORF138; ORF189; ORF190; ORF233; ORF246; ORF338; ORF412;ORF421; ORF438; ORF607; ORF648; ORF657; ORF740; ORF783; ORF967; ORF989;ORF990; ORF992; ORF1011; ORF1058; ORF1059; ORF1073; ORF1074 and one oftheir representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the metabolism of nucleic acids, such as forexample DNA polymerases or DNA topoisomerases, and in that they comprisea nucleotide sequence chosen from the following sequences:

ORF14; ORF59; ORF70; ORF71; ORF97; ORF113; ORF137; ORF141; ORF169;ORF285; ORF287; ORF288; ORF313; ORF326; ORF358; ORF411; ORF443; ORF548;ORF569; ORF601; ORF651; ORF654; ORF658; ORF659; ORF664; ORF665; ORF694;ORF698; ORF704; ORF760; ORF762; ORF763; ORF786; ORF787; ORF788; ORF801;ORF802; ORF812; ORF819; ORF822; ORF870; ORF897; ORF898; ORF902; ORF908;ORF916; ORF954; ORF955; ORF961; ORF983; ORF996; ORF1007; ORF1012;ORF1013; ORF1014; ORF1015; ORF1038; ORF1137 and one of theirrepresentative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the metabolism of amino acids or polypeptides, suchas for example serine hydroxymethyl transferase or the proteins whichload amino acids onto transfer RNAs, and in that they comprise anucleotide sequence chosen from the following sequences:

ORF99; ORF111; ORF127; ORF134; ORF140; ORF174; ORF175; ORF176; ORF353;ORF377; ORF404; ORF523; ORF539; ORF559; ORF561; ORF586; ORF598; ORF609;ORF636; ORF687; ORF700; ORF701; ORF759; ORF790; ORF857; ORF861; ORF904;ORF936; ORF952; ORF962; ORF963; ORF964; ORF965; ORF991; ORF1003;ORF1004; ORF1005; ORF1018; ORF1067; ORF1110; ORF1111; ORF1112; ORF1114;ORF1121; ORF1122; ORF1123; ORF1124; ORF1125 and one of theirrepresentative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the metabolism of polypeptides, such as for exampleprotein kinases or proteases, and in that they comprise a nucleotidesequence chosen from the following sequences:

ORF4; ORF44; ORF45; ORF48; ORF54; ORF112; ORF130; ORF155; ORF163;ORF212; ORF257; ORF307; ORF343; ORF405; ORF416; ORF458; ORF540; ORF541;ORF542; ORF543; ORF544; ORF560; ORF594; ORF652; ORF699; ORF723; ORF747;ORF817; ORF827; ORF871; ORF909; ORF910; ORF911; ORF912; ORF1023;ORF1051; ORF1052; ORF1081 and one of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the metabolism of fatty acids, such as for examplesuccinyl-CoA-synthesizing proteins or phosphatidylserine synthetase, andin that they comprise a nucleotide sequence chosen from the followingsequences:

ORF76; ORF284; ORF308; ORF309; ORF310; ORF311; ORF312; ORF425; ORF433;ORF565; ORF688; ORF690; ORF691; ORF767; ORF797; ORF894; ORF895; ORF994;ORF1020; ORF1030; ORF1033; ORF1034; ORF1046; ORF1047; ORF1057 and one oftheir representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the synthesis of the wall, such as for example KDOtransferase, and the proteins responsible for the attachment of certainsugars onto the exposed proteins, and in that they comprise a nucleotidesequence chosen from the following sequences:

ORF49; ORF50; ORF177; ORF178; ORF245; ORF610; ORF972; ORF974; ORF978;ORF1037 and one of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the transcription, translation and/or maturationprocess, such as for example initiation factors, RNA polymerases orcertain chaperone proteins, and in that they comprise a nucleotidesequence chosen from the following sequences:

ORF90; ORF92; ORF131; ORF151; ORF199; ORF333; ORF334; ORF336; ORF379;ORF589; ORF590; ORF619; ORF630; ORF649; ORF739; ORF741; ORF806; ORF821;ORF843; ORF968; ORF971; ORF1061 and one of their representativefragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae ribosomal polypeptide or one of its representativefragments, such as for example the ribosomal proteins L21, L27 and S10,and in that they comprise a nucleotide sequence chosen from thefollowing sequences:

ORF93; ORF94; ORF95; ORF136; ORF259; ORF332; ORF348; ORF583; ORF584;ORF588; ORF591; ORF592; ORF663; ORF666; ORF667; ORF669; ORF670; ORF671;ORF672; ORF673; ORF674; ORF675; ORF676; ORF677; ORF678; ORF679; ORF680;ORF681; ORF683; ORF684; ORF738; ORF781; ORF1008; ORF1024; ORF1025;ORF1066 and one of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae transport polypeptide or one of its representativefragments, such as for example the proteins for transporting aminoacids, sugars and certain oligopeptides, and in that they comprise anucleotide sequence chosen from the following sequences:

ORF40; ORF41; ORF52; ORF105; ORF106; ORF107; ORF109; ORF133; ORF210;ORF211; ORF214; ORF215; ORF216; ORF217; ORF218; ORF219; ORF220; ORF223;ORF242; ORF260; ORF293; ORF299; ORF366; ORF369; ORF575; ORF602; ORF638;ORF639; ORF640; ORF643; ORF653; ORF702; ORF703; ORF724; ORF732; ORF855;ORF856; ORF901; ORF906; ORF933; ORF942; ORF1043; ORF1086; ORF1105 andone of their representative fragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the virulence process, such as for example theproteins analogous to the Escherichia coli vacB protein, and in thatthey comprise a nucleotide sequence chosen from the following sequences:

ORF546; ORF550; ORF778; ORF779; ORF886 and one of their representativefragments.

Preferably, the invention also relates to the nucleotide sequencesaccording to the invention, characterized in that they encode aChlamydia pneumoniae polypeptide or one of its representative fragmentswhich is involved in the secretory system and/or which is secreted, suchas for example proteins homologous to proteins in the secretory systemof certain bacteria such as the Salmonellae or the Yersiniae, and inthat they comprise a nucleotide sequence chosen from the followingsequences:

ORF751; ORF874; ORF875; ORF876; ORF883; ORF884; ORF885 and one of theirrepresentative fragments.

Preferably, the invention also relates to a nucleotide sequenceaccording to the invention, characterized in that they encode apolypeptide specific to Chlamydia pneumoniae or one of itsrepresentative fragments (with a Blast E value of >10⁻⁵), and in thatthey comprise a nucleotide sequence chosen from the following sequences:

ORF7; ORF8; ORF17; ORF18; ORF19; ORF20; ORF22; ORF23; ORF24; ORF51;ORF60; ORF63; ORF65; ORF66; ORF67; ORF83; ORF84; ORF86; ORF87; ORF125;ORF143; ORF144; ORF179; ORF182; ORF184; ORF185; ORF187; ORF221; ORF252;ORF254; ORF278; ORF279; ORF387; ORF388; ORF397; ORF1048; ORF1049;ORF1050; ORF1128; ORF1130; ORF1131 and one of their representativefragments.

Also forming part of the invention are polypeptides encoded by thepolynucleotides of the invention, as well as fusion polypeptidescomprising such polypeptides. In one embodiment, the polypeptides andfusion polypeptides immunoreact with seropositive serum of an individualinfected with Chlamydia pneumoniae. For example, described below, arepolypeptide sequences exhibiting particularly preferablecharacteristics. For each group of preferred polypeptides describedbelow, it is to be understood that in addition to the individualpolypeptides listed, in instances wherein such polypeptides are encodedas part of “combined” ORFs, such “combined” polypeptides are also to beincluded within the preferred group.

The subject of the invention is also a polypeptide according to theinvention, characterized in that it is a polypeptide of the cellularenvelope, preferably of the outer cellular envelope, of Chlamydiapneumoniae or one of its representative fragments. According to theinvention, the said polypeptide is preferably chosen from thepolypeptides having the following sequences:

SEQ ID No. 15; SEQ ID No. 25; SEQ ID No. 26; SEQ ID No. 27; SEQ ID No.28; SEQ ID No. 29; SEQ ID No. 30; SEQ ID No. 31; SEQ ID No. 32; SEQ IDNo. 33; SEQ ID No. 35; SEQ ID No. 68; SEQ ID No. 124; SEQ ID No. 275;SEQ ID No. 291; SEQ ID No. 294; SEQ ID No. 327; SEQ ID No. 342; SEQ IDNo. 364; SEQ ID No. 374; SEQ ID No. 380; SEQ ID No. 414; SEQ ID No. 439;SEQ ID No. 466; SEQ ID No. 467; SEQ ID No. 468; SEQ ID No. 469; SEQ IDNo. 470; SEQ ID No. 472; SEQ ID No. 474; SEQ ID No. 476; SEQ ID No. 477;SEQ ID No. 478; SEQ ID No. 479; SEQ ID No. 480; SEQ ID No. 482; SEQ IDNo. 485; SEQ ID No. 500; SEQ ID No. 501; SEQ ID No. 503; SEQ ID No. 504;SEQ ID No. 505; SEQ ID No. 506; SEQ ID No. 520; SEQ ID No. 578; SEQ IDNo. 580; SEQ ID No. 581; SEQ ID No. 595; SEQ ID No. 596; SEQ ID No. 597;SEQ ID No. 737; SEQ ID No. 830; SEQ ID No. 834; SEQ ID No. 836; SEQ IDNo. 893; SEQ ID No. 917; SEQ ID No. 932; SEQ ID No. 976; SEQ ID No.1035; SEQ ID No. 1045; SEQ ID No. 1090 and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaetransmembrane polypeptide or one of its representative fragments, havingbetween 1 and 3 transmembrane domains, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 2; SEQ ID No. 3; SEQ ID No. 6; SEQ ID No. 9; SEQ ID No. 10;SEQ ID No. 11; SEQ ID No. 13; SEQ ID No. 14; SEQ ID No. 16; SEQ ID No.18; SEQ ID No. 19; SEQ ID No. 20; SEQ ID No. 21; SEQ ID No. 22; SEQ IDNo. 25; SEQ ID No. 27; SEQ ID No. 28; SEQ ID No. 29; SEQ ID No. 30; SEQID No. 31; SEQ ID No. 32; SEQ ID No. 33; SEQ ID No. 34; SEQ ID No. 35;SEQ ID No. 37; SEQ ID No. 39; SEQ ID No. 41; SEQ ID No. 42; SEQ ID No.44; SEQ ID No. 45; SEQ ID No. 46; SEQ ID No. 47; SEQ ID No. 48; SEQ IDNo. 49; SEQ ID No. 50; SEQ ID No. 53; SEQ ID No. 54; SEQ ID No. 56; SEQID No. 57; SEQ ID No. 59; SEQ ID No. 60; SEQ ID No. 61; SEQ ID No. 62;SEQ ID No. 63; SEQ ID No. 64; SEQ ID No. 65; SEQ ID No. 66; SEQ ID No.69; SEQ ID No. 72; SEQ ID No. 73; SEQ ID No. 74; SEQ ID No. 76; SEQ IDNo. 77; SEQ ID No. 78; SEQ ID No. 79; SEQ ID No. 80; SEQ ID No. 82; SEQID No. 84; SEQ ID No. 85; SEQ ID No. 86; SEQ ID No. 88; SEQ ID No. 89;SEQ ID No. 90; SEQ ID No. 91; SEQ ID No. 92; SEQ ID No. 93; SEQ ID No.95; SEQ ID No. 96; SEQ ID No. 98; SEQ ID No. 99; SEQ ID No. 100; SEQ IDNo. 101; SEQ ID No. 102; SEQ ID No. 103; SEQ ID No. 104; SEQ ID No. 105;SEQ ID No. 106; SEQ ID No. 107; SEQ ID No. 108; SEQ ID No. 114; SEQ IDNo. 117; SEQ ID No. 118; SEQ ID No. 122; SEQ ID No. 123; SEQ ID No. 124;SEQ ID No. 125; SEQ ID No. 129; SEQ ID No. 130; SEQ ID No. 131; SEQ IDNo. 132; SEQ ID No. 133; SEQ ID No. 134; SEQ ID No. 135; SEQ ID No. 137;SEQ ID No. 138; SEQ ID No. 139; SEQ ID No. 140; SEQ ID No. 141; SEQ IDNo. 142; SEQ ID No. 143; SEQ ID No. 145; SEQ ID No. 146; SEQ ID No. 147;SEQ ID No. 150; SEQ ID No. 151; SEQ ID No. 152; SEQ ID No. 156; SEQ IDNo. 157; SEQ ID No. 158; SEQ ID No. 159; SEQ ID No. 160; SEQ ID No. 161;SEQ ID No. 162; SEQ ID No. 164; SEQ ID No. 166; SEQ ID No. 167; SEQ IDNo. 170; SEQ ID No. 173; SEQ ID No. 175; SEQ ID No. 176; SEQ ID No. 178;SEQ ID No. 179; SEQ ID No. 180; SEQ ID No. 182; SEQ ID No. 183; SEQ IDNo. 184; SEQ ID No. 185; SEQ ID No. 186; SEQ ID No. 187; SEQ ID No. 188;SEQ ID No. 189; SEQ ID No. 190; SEQ ID No. 191; SEQ ID No. 192; SEQ IDNo. 194; SEQ ID No. 195; SEQ ID No. 196; SEQ ID No. 197; SEQ ID No. 198;SEQ ID No. 199; SEQ ID No. 200; SEQ ID No. 201; SEQ ID No. 202; SEQ IDNo. 205; SEQ ID No. 207; SEQ ID No. 208; SEQ ID No. 209; SEQ ID No. 210;SEQ ID No. 212; SEQ ID No. 215; SEQ ID No. 219; SEQ ID No. 220; SEQ IDNo. 224; SEQ ID No. 226; SEQ ID No. 227; SEQ ID No. 228; SEQ ID No. 231;SEQ ID No. 232; SEQ ID No. 233; SEQ ID No. 234; SEQ ID No. 235; SEQ IDNo. 236; SEQ ID No. 238; SEQ ID No. 239; SEQ ID No. 240; SEQ ID No. 241;SEQ ID No. 242; SEQ ID No. 244; SEQ ID No. 247; SEQ ID No. 251; SEQ IDNo. 252; SEQ ID No. 253; SEQ ID No. 255; SEQ ID No. 256; SEQ ID No. 257;SEQ ID No. 258; SEQ ID No. 260; SEQ ID No. 262; SEQ ID No. 263; SEQ IDNo. 266; SEQ ID No. 267; SEQ ID No. 268; SEQ ID No. 269; SEQ ID No. 270;SEQ ID No. 273; SEQ ID No. 274; SEQ ID No. 276; SEQ ID No. 278; SEQ IDNo. 279; SEQ ID No. 280; SEQ ID No. 281; SEQ ID No. 282; SEQ ID No. 283;SEQ ID No. 284; SEQ ID No. 286; SEQ ID No. 287; SEQ ID No. 289; SEQ IDNo. 290; SEQ ID No. 291; SEQ ID No. 293; SEQ ID No. 294; SEQ ID No. 297;SEQ ID No. 304; SEQ ID No. 305; SEQ ID No. 307; SEQ ID No. 308; SEQ IDNo. 309; SEQ ID No. 310; SEQ ID No. 311; SEQ ID No. 313; SEQ ID No. 314;SEQ ID No. 315; SEQ ID No. 316; SEQ ID No. 318; SEQ ID No. 319; SEQ IDNo. 320; SEQ ID No. 321; SEQ ID No. 322; SEQ ID No. 323; SEQ ID No. 324;SEQ ID No. 325; SEQ ID No. 326; SEQ ID No. 331; SEQ ID No. 332; SEQ IDNo. 336; SEQ ID No. 338; SEQ ID No. 339; SEQ ID No. 341; SEQ ID No. 344;SEQ ID No. 345; SEQ ID No. 346; SEQ ID No. 350; SEQ ID No. 352; SEQ IDNo. 353; SEQ ID No. 356; SEQ ID No. 357; SEQ ID No. 358; SEQ ID No. 359;SEQ ID No. 360; SEQ ID No. 362; SEQ ID No. 365; SEQ ID No. 366; SEQ IDNo. 367; SEQ ID No. 370; SEQ ID No. 372; SEQ ID No. 373; SEQ ID No. 376;SEQ ID No. 377; SEQ ID No. 378; SEQ ID No. 379; SEQ ID No. 381; SEQ IDNo. 382; SEQ ID No. 383; SEQ ID No. 384; SEQ ID No. 385; SEQ ID No. 386;SEQ ID No. 387; SEQ ID No. 390; SEQ ID No. 392; SEQ ID No. 393; SEQ IDNo. 394; SEQ ID No. 396; SEQ ID No. 398; SEQ ID No. 399; SEQ ID No. 400;SEQ ID No. 404; SEQ ID No. 408; SEQ ID No. 410; SEQ ID No. 411; SEQ IDNo. 413; SEQ ID No. 416; SEQ ID No. 417; SEQ ID No. 418; SEQ ID No. 420;SEQ ID No. 422; SEQ ID No. 424; SEQ ID No. 427; SEQ ID No. 428; SEQ IDNo. 429; SEQ ID No. 430; SEQ ID No. 431; SEQ ID No. 433; SEQ ID No. 434;SEQ ID No. 437; SEQ ID No. 440; SEQ ID No. 441; SEQ ID No. 442; SEQ IDNo. 443; SEQ ID No. 444; SEQ ID No. 445; SEQ ID No. 447; SEQ ID No. 450;SEQ ID No. 451; SEQ ID No. 452; SEQ ID No. 455; SEQ ID No. 456; SEQ IDNo. 459; SEQ ID No. 460; SEQ ID No. 461; SEQ ID No. 462; SEQ ID No. 463;SEQ ID No. 464; SEQ ID No. 465; SEQ ID No. 467; SEQ ID No. 469; SEQ IDNo. 471; SEQ ID No. 474; SEQ ID No. 475; SEQ ID No. 476; SEQ ID No. 477;SEQ ID No. 479; SEQ ID No. 482; SEQ ID No. 483; SEQ ID No. 484; SEQ IDNo. 485; SEQ ID No. 486; SEQ ID No. 487; SEQ ID No. 488; SEQ ID No. 491;SEQ ID No. 493; SEQ ID No. 494; SEQ ID No. 497; SEQ ID No. 498; SEQ IDNo. 499; SEQ ID No. 503; SEQ ID No. 508; SEQ ID No. 509; SEQ ID No. 510;SEQ ID No. 512; SEQ ID No. 514; SEQ ID No. 515; SEQ ID No. 516; SEQ IDNo. 517; SEQ ID No. 518; SEQ ID No. 520; SEQ ID No. 521; SEQ ID No. 523;SEQ ID No. 525; SEQ ID No. 527; SEQ ID No. 528; SEQ ID No. 529; SEQ IDNo. 530; SEQ ID No. 531; SEQ ID No. 533; SEQ ID No. 534; SEQ ID No. 535;SEQ ID No. 536; SEQ ID No. 537; SEQ ID No. 540; SEQ ID No. 541; SEQ IDNo. 543; SEQ ID No. 544; SEQ ID No. 545; SEQ ID No. 546; SEQ ID No. 548;SEQ ID No. 549; SEQ ID No. 551; SEQ ID No. 553; SEQ ID No. 554; SEQ IDNo. 555; SEQ ID No. 556; SEQ ID No. 557; SEQ ID No. 558; SEQ ID No. 559;SEQ ID No. 560; SEQ ID No. 562; SEQ ID No. 563; SEQ ID No. 564; SEQ IDNo. 565; SEQ ID No. 566; SEQ ID No. 569; SEQ ID No. 571; SEQ ID No. 573;SEQ ID No. 576; SEQ ID No. 577; SEQ ID No. 581; SEQ ID No. 583; SEQ IDNo. 584; SEQ ID No. 585; SEQ ID No. 586; SEQ ID No. 588; SEQ ID No. 591;SEQ ID No. 592; SEQ ID No. 594; SEQ ID No. 595; SEQ ID No. 596; SEQ IDNo. 597; SEQ ID No. 599; SEQ ID No. 600; SEQ ID No. 603; SEQ ID No. 605;SEQ ID No. 608; SEQ ID No. 614; SEQ ID No. 615; SEQ ID No. 620; SEQ IDNo. 621; SEQ ID No. 622; SEQ ID No. 623; SEQ ID No. 624; SEQ ID No. 625;SEQ ID No. 629; SEQ ID No. 630; SEQ ID No. 631; SEQ ID No. 633; SEQ IDNo. 634; SEQ ID No. 637; SEQ ID No. 642; SEQ ID No. 644; SEQ ID No. 645;SEQ ID No. 647; SEQ ID No. 648; SEQ ID No. 652; SEQ ID No. 654; SEQ IDNo. 655; SEQ ID No. 657; SEQ ID No. 658; SEQ ID No. 659; SEQ ID No. 660;SEQ ID No. 661; SEQ ID No. 664; SEQ ID No. 665; SEQ ID No. 666; SEQ IDNo. 667; SEQ ID No. 670; SEQ ID No. 671; SEQ ID No. 672; SEQ ID No. 673;SEQ ID No. 674; SEQ ID No. 676; SEQ ID No. 679; SEQ ID No. 681; SEQ IDNo. 684; SEQ ID No. 687; SEQ ID No. 688; SEQ ID No. 689; SEQ ID No. 690;SEQ ID No. 693; SEQ ID No. 694; SEQ ID No. 695; SEQ ID No. 696; SEQ IDNo. 697; SEQ ID No. 698; SEQ ID No. 699; SEQ ID No. 700; SEQ ID No. 701;SEQ ID No. 703; SEQ ID No. 705; SEQ ID No. 706; SEQ ID No. 707; SEQ IDNo. 708; SEQ ID No. 710; SEQ ID No. 712; SEQ ID No. 715; SEQ ID No. 716;SEQ ID No. 717; SEQ ID No. 718; SEQ ID No. 719; SEQ ID No. 721; SEQ IDNo. 722; SEQ ID No. 723; SEQ ID No. 725; SEQ ID No. 726; SEQ ID No. 727;SEQ ID No. 728; SEQ ID No. 729; SEQ ID No. 730; SEQ ID No. 731; SEQ IDNo. 733; SEQ ID No. 736; SEQ ID No. 737; SEQ ID No. 738; SEQ ID No. 740;SEQ ID No. 741; SEQ ID No. 742; SEQ ID No. 743; SEQ ID No. 747; SEQ IDNo. 748; SEQ ID No. 750; SEQ ID No. 752; SEQ ID No. 754; SEQ ID No. 755;SEQ ID No. 756; SEQ ID No. 757; SEQ ID No. 759; SEQ ID No. 760; SEQ IDNo. 761; SEQ ID No. 762; SEQ ID No. 763; SEQ ID No. 764; SEQ ID No. 765;SEQ ID No. 766; SEQ ID No. 767; SEQ ID No. 768; SEQ ID No. 772; SEQ IDNo. 774; SEQ ID No. 775; SEQ ID No. 777; SEQ ID No. 781; SEQ ID No. 783;SEQ ID No. 788; SEQ ID No. 791; SEQ ID No. 792; SEQ ID No. 793; SEQ IDNo. 794; SEQ ID No. 795; SEQ ID No. 796; SEQ ID No. 797; SEQ ID No. 798;SEQ ID No. 799; SEQ ID No. 802; SEQ ID No. 803; SEQ ID No. 806; SEQ IDNo. 807; SEQ ID No. 808; SEQ ID No. 809; SEQ ID No. 810; SEQ ID No. 811;SEQ ID No. 813; SEQ ID No. 814; SEQ ID No. 815; SEQ ID No. 816; SEQ IDNo. 817; SEQ ID No. 819; SEQ ID No. 820; SEQ ID No. 821; SEQ ID No. 823;SEQ ID No. 824; SEQ ID No. 827; SEQ ID No. 829; SEQ ID No. 830; SEQ IDNo. 831; SEQ ID No. 833; SEQ ID No. 834; SEQ ID No. 835; SEQ ID No. 837;SEQ ID No. 844; SEQ ID No. 845; SEQ ID No. 846; SEQ ID No. 847; SEQ IDNo. 848; SEQ ID No. 849; SEQ ID No. 850; SEQ ID No. 851; SEQ ID No. 852;SEQ ID No. 854; SEQ ID No. 855; SEQ ID No. 856; SEQ ID No. 857; SEQ IDNo. 859; SEQ ID No. 860; SEQ ID No. 862; SEQ ID No. 865; SEQ ID No. 866;SEQ ID No. 868; SEQ ID No. 869; SEQ ID No. 870; SEQ ID No. 871; SEQ IDNo. 872; SEQ ID No. 874; SEQ ID No. 877; SEQ ID No. 878; SEQ ID No. 879;SEQ ID No. 880; SEQ ID No. 881; SEQ ID No. 882; SEQ ID No. 884; SEQ IDNo. 885; SEQ ID No. 888; SEQ ID No. 889; SEQ ID No. 890; SEQ ID No. 891;SEQ ID No. 892; SEQ ID No. 894; SEQ ID No. 895; SEQ ID No. 896; SEQ IDNo. 897; SEQ ID No. 899; SEQ ID No. 900; SEQ ID No. 902; SEQ ID No. 903;SEQ ID No. 904; SEQ ID No. 905; SEQ ID No. 909; SEQ ID No. 910; SEQ IDNo. 912; SEQ ID No. 913; SEQ ID No. 914; SEQ ID No. 915; SEQ ID No. 917;SEQ ID No. 918; SEQ ID No. 919; SEQ ID No. 921; SEQ ID No. 923; SEQ IDNo. 924; SEQ ID No. 926; SEQ ID No. 927; SEQ ID No. 928; SEQ ID No. 929;SEQ ID No. 930; SEQ ID No. 931; SEQ ID No. 937; SEQ ID No. 938; SEQ IDNo. 939; SEQ ID No. 941; SEQ ID No. 943; SEQ ID No. 948; SEQ ID No. 951;SEQ ID No. 952; SEQ ID No. 953; SEQ ID No. 958; SEQ ID No. 960; SEQ IDNo. 963; SEQ ID No. 964; SEQ ID No. 965; SEQ ID No. 968; SEQ ID No. 970;SEQ ID No. 974; SEQ ID No. 975; SEQ ID No. 977; SEQ ID No. 979; SEQ IDNo. 980; SEQ ID No. 981; SEQ ID No. 983; SEQ ID No. 984; SEQ ID No. 985;SEQ ID No. 987; SEQ ID No. 989; SEQ ID No. 992; SEQ ID No. 993; SEQ IDNo. 997; SEQ ID No. 998; SEQ ID No. 999; SEQ ID No. 1001; SEQ ID No.1002; SEQ ID No. 1004; SEQ ID No. 1005; SEQ ID No. 1009; SEQ ID No.1013; SEQ ID No. 1014; SEQ ID No. 1015; SEQ ID No. 1016; SEQ ID No.1019; SEQ ID No. 1021; SEQ ID No. 1023; SEQ ID No. 1024; SEQ ID No.1029; SEQ ID No. 1031; SEQ ID No. 1033; SEQ ID No. 1034; SEQ ID No.1039; SEQ ID No. 1041; SEQ ID No. 1042; SEQ ID No. 1045; SEQ ID No.1047; SEQ ID No. 1049; SEQ ID No. 1051; SEQ ID No. 1052; SEQ ID No.1053; SEQ ID No. 1054; SEQ ID No. 1056; SEQ ID No. 1059; SEQ ID No.1061; SEQ ID No. 1062; SEQ ID No. 1063; SEQ ID No. 1064; SEQ ID No.1065; SEQ ID No. 1067; SEQ ID No. 1075; SEQ ID No. 1077; SEQ ID No.1078; SEQ ID No. 1079; SEQ ID No. 1080; SEQ ID No. 1081; SEQ ID No.1089; SEQ ID No. 1095; SEQ ID No. 1097; SEQ ID No. 1098; SEQ ID No.1099; SEQ ID No. 1101; SEQ ID No. 1102; SEQ ID No. 1103; SEQ ID No.1106; SEQ ID No. 1107; SEQ ID No. 1108; SEQ ID No. 1109; SEQ ID No.1110; SEQ ID No. 1113; SEQ ID No. 1116; SEQ ID No. 1118; SEQ ID No.1119; SEQ ID No. 1121; SEQ ID No. 1123; SEQ ID No. 1124; SEQ ID No.1126; SEQ ID No. 1128; SEQ ID No. 1130; SEQ ID No. 1131; SEQ ID No.1133; SEQ ID No. 1134; SEQ ID No. 1136; SEQ ID No. 1137 and one of theirrepresentative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaetransmembrane polypeptide or one of its respective fragments, havingbetween 4 and 6 transmembrane domains, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 5; SEQ ID No. 7; SEQ ID No. 8; SEQ ID No. 15; SEQ ID No. 36;SEQ ID No. 38; SEQ ID No. 51; SEQ ID No. 55; SEQ ID No. 58; SEQ ID No.67; SEQ ID No. 70; SEQ ID No. 81; SEQ ID No. 97; SEQ ID No. 110; SEQ IDNo. 111; SEQ ID No. 115; SEQ ID No. 119; SEQ ID No. 126; SEQ ID No. 128;SEQ ID No. 148; SEQ ID No. 155; SEQ ID No. 163; SEQ ID No. 165; SEQ IDNo. 168; SEQ ID No. 169; SEQ ID No. 171; SEQ ID No. 172; SEQ ID No. 174;SEQ ID No. 177; SEQ ID No. 181; SEQ ID No. 193; SEQ ID No. 203; SEQ IDNo. 213; SEQ ID No. 214; SEQ ID No. 216; SEQ ID No. 217; SEQ ID No. 221;SEQ ID No. 222; SEQ ID No. 225; SEQ ID No. 229; SEQ ID No. 243; SEQ IDNo. 246; SEQ ID No. 248; SEQ ID No. 254; SEQ ID No. 261; SEQ ID No. 285;SEQ ID No. 288; SEQ ID No. 292; SEQ ID No. 296; SEQ ID No. 298; SEQ IDNo. 299; SEQ ID No. 301; SEQ ID No. 303; SEQ ID No. 317; SEQ ID No. 328;SEQ ID No. 329; SEQ ID No. 351; SEQ ID No. 354; SEQ ID No. 355; SEQ IDNo. 364; SEQ ID No. 371; SEQ ID No. 374; SEQ ID No. 375; SEQ ID No. 391;SEQ ID No. 395; SEQ ID No. 401; SEQ ID No. 403; SEQ ID No. 405; SEQ IDNo. 409; SEQ ID No. 414; SEQ ID No. 419; SEQ ID No. 421; SEQ ID No. 423;SEQ ID No. 425; SEQ ID No. 438; SEQ ID No. 448; SEQ ID No. 453; SEQ IDNo. 458; SEQ ID No. 466; SEQ ID No. 468; SEQ ID No. 470; SEQ ID No. 480;SEQ ID No. 489; SEQ ID No. 490; SEQ ID No. 496; SEQ ID No. 501; SEQ IDNo. 504; SEQ ID No. 505; SEQ ID No. 506; SEQ ID No. 511; SEQ ID No. 513;SEQ ID No. 519; SEQ ID No. 526; SEQ ID No. 532; SEQ ID No. 538; SEQ IDNo. 539; SEQ ID No. 547; SEQ ID No. 550; SEQ ID No. 561; SEQ ID No. 568;SEQ ID No. 570; SEQ ID No. 574; SEQ ID No. 578; SEQ ID No. 579; SEQ IDNo. 580; SEQ ID No. 582; SEQ ID No. 589; SEQ ID No. 593; SEQ ID No. 598;SEQ ID No. 601; SEQ ID No. 604; SEQ ID No. 610; SEQ ID No. 613; SEQ IDNo. 617; SEQ ID No. 626; SEQ ID No. 632; SEQ ID No. 635; SEQ ID No. 638;SEQ ID No. 640; SEQ ID No. 641; SEQ ID No. 646; SEQ ID No. 649; SEQ IDNo. 650; SEQ ID No. 651; SEQ ID No. 686; SEQ ID No. 711; SEQ ID No. 724;SEQ ID No. 732; SEQ ID No. 734; SEQ ID No. 744; SEQ ID No. 745; SEQ IDNo. 749; SEQ ID No. 751; SEQ ID No. 769; SEQ ID No. 770; SEQ ID No. 771;SEQ ID No. 773; SEQ ID No. 776; SEQ ID No. 779; SEQ ID No. 780; SEQ IDNo. 785; SEQ ID No. 787; SEQ ID No. 789; SEQ ID No. 801; SEQ ID No. 805;SEQ ID No. 812; SEQ ID No. 822; SEQ ID No. 825; SEQ ID No. 826; SEQ IDNo. 839; SEQ ID No. 841; SEQ ID No. 843; SEQ ID No. 853; SEQ ID No. 861;SEQ ID No. 875; SEQ ID No. 876; SEQ ID No. 886; SEQ ID No. 893; SEQ IDNo. 898; SEQ ID No. 906; SEQ ID No. 907; SEQ ID No. 908; SEQ ID No. 920;SEQ ID No. 922; SEQ ID No. 925; SEQ ID No. 933; SEQ ID No. 935; SEQ IDNo. 936; SEQ ID No. 944; SEQ ID No. 946; SEQ ID No. 947; SEQ ID No. 954;SEQ ID No. 959; SEQ ID No. 961; SEQ ID No. 966; SEQ ID No. 967; SEQ IDNo. 972; SEQ ID No. 978; SEQ ID No. 995; SEQ ID No. 996; SEQ ID No.1000; SEQ ID No. 1003; SEQ ID No. 1010; SEQ ID No. 1011; SEQ ID No.1012; SEQ ID No. 1017; SEQ ID No. 1020; SEQ ID No. 1030; SEQ ID No.1036; SEQ ID No. 1038; SEQ ID No. 1043; SEQ ID No. 1046; SEQ ID No.1048; SEQ ID No. 1050; SEQ ID No. 1058; SEQ ID No. 1071; SEQ ID No.1073; SEQ ID No. 1084; SEQ ID No. 1085; SEQ ID No. 1086; SEQ ID No.1087; SEQ ID No. 1091; SEQ ID No. 1092; SEQ ID No. 1094; SEQ ID No.1096; SEQ ID No. 1100; SEQ ID No. 1104; SEQ ID No. 1111; SEQ ID No.1112; SEQ ID No. 1114; SEQ ID No. 1117; SEQ ID No. 1122; SEQ ID No. 1125and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaetransmembrane polypeptide or one of its representative fragments, havingat least 7 transmembrane domains, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 17; SEQ ID No. 52; SEQ ID No. 68; SEQ ID No. 83; SEQ ID No.87; SEQ ID No. 109; SEQ ID No. 112; SEQ ID No. 113; SEQ ID No. 120; SEQID No. 121; SEQ ID No. 127; SEQ ID No. 153; SEQ ID No. 204; SEQ ID No.211; SEQ ID No. 218; SEQ ID No. 223; SEQ ID No. 275; SEQ ID No. 277; SEQID No. 295; SEQ ID No. 300; SEQ ID No. 302; SEQ ID No. 306; SEQ ID No.327; SEQ ID No. 335; SEQ ID No. 342; SEQ ID No. 343; SEQ ID No. 347; SEQID No. 349; SEQ ID No. 361; SEQ ID No. 363; SEQ ID No. 369; SEQ ID No.380; SEQ ID No. 388; SEQ ID No. 389; SEQ ID No. 397; SEQ ID No. 415; SEQID No. 432; SEQ ID No. 439; SEQ ID No. 446; SEQ ID No. 449; SEQ ID No.472; SEQ ID No. 478; SEQ ID No. 500; SEQ ID No. 522; SEQ ID No. 524; SEQID No. 567; SEQ ID No. 575; SEQ ID No. 602; SEQ ID No. 606; SEQ ID No.609; SEQ ID No. 636; SEQ ID No. 639; SEQ ID No. 643; SEQ ID No. 653; SEQID No. 668; SEQ ID No. 692; SEQ ID No. 702; SEQ ID No. 704; SEQ ID No.713; SEQ ID No. 720; SEQ ID No. 778; SEQ ID No. 784; SEQ ID No. 800; SEQID No. 836; SEQ ID No. 838; SEQ ID No. 842; SEQ ID No. 864; SEQ ID No.867; SEQ ID No. 883; SEQ ID No. 901; SEQ ID No. 916; SEQ ID No. 932; SEQID No. 934; SEQ ID No. 940; SEQ ID No. 942; SEQ ID No. 950; SEQ ID No.956; SEQ ID No. 971; SEQ ID No. 973; SEQ ID No. 976; SEQ ID No. 988; SEQID No. 994; SEQ ID No. 1018; SEQ ID No. 1028; SEQ ID No. 1035; SEQ IDNo. 1037; SEQ ID No. 1044; SEQ ID No. 1055; SEQ ID No. 1057; SEQ ID No.1068; SEQ ID No. 1069; SEQ ID No. 1070; SEQ ID No. 1072; SEQ ID No.1082; SEQ ID No. 1088; SEQ ID No. 1105; SEQ ID No. 1132; SEQ ID No. 1135and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae surface exposedpolypeptide or one of its representative fragments, and in that it ischosen from the polypeptides having the following sequences:

SEQ ID No. 15, SEQ ID No. 25, SEQ ID No. 26, SEQ ID No. 27, SEQ ID No.28, SEQ ID No. 29, SEQ ID No. 30, SEQ ID No. 31, SEQ ID No. 32, SEQ IDNo. 33, SEQ ID No. 35, SEQ ID No. 36, SEQ ID No. 1257, SEQ ID No. 280,SEQ ID No. 291, SEQ ID No. 314, SEQ ID No. 354, SEQ ID No. 380, SEQ IDNo. 1266, SEQ ID No. 466, SEQ ID No. 467, SEQ ID No. 468, SEQ ID No.469, SEQ ID No. 470, SEQ ID No. 472, SEQ ID No. 474, SEQ ID No. 476, SEQID No. 477, SEQ ID No. 478, SEQ ID No. 479, SEQ ID No. 480, SEQ ID No.482, SEQ ID No. 483, SEQ ID No. 485, SEQ ID No. 486, SEQ ID No. 500, SEQID No. 501, SEQ ID No. 503, SEQ ID No. 504, SEQ ID No. 505, SEQ ID No.506, SEQ ID No. 507, SEQ ID No. 1268, SEQ ID No. 1269, SEQ ID No. 543,SEQ ID No. 544, SEQ ID No. 578, SEQ ID No. 579, SEQ ID No. 580, SEQ IDNo. 581, SEQ ID No. 595, SEQ ID No. 596, SEQ ID No. 597, SEQ ID No.1271, SEQ ID No. 633, SEQ ID No. 637, SEQ ID No. 699, SEQ ID No. 706,SEQ ID No. 737, SEQ ID No. 744, SEQ ID No. 1273, SEQ ID No. 751, SEQ IDNo. 775, SEQ ID No. 776, SEQ ID No. 777, SEQ ID No. 793, SEQ ID No. 815,SEQ ID No. 830, SEQ ID No. 1221, SEQ ID No. 849, SEQ ID No. 851, SEQ IDNo. 852, SEQ ID No. 874, SEQ ID No. 891, SEQ ID No. 922, SEQ ID No. 940,SEQ ID No. 1231, SEQ ID No. 1281, SEQ ID No. 1035, SEQ ID No. 1079, SEQID No. 1087, SEQ ID No. 1108, and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaelipoprotein or one of its representative fragments, and in that it ischosen from the polypeptides having the following sequences:

SEQ ID No. 3, SEQ ID No. 10, SEQ ID No. 11, SEQ ID No. 16, SEQ ID No.1254, SEQ ID No. 1255, SEQ ID No. 38, SEQ ID No. 1256, SEQ ID No. 62,SEQ ID No. 85, SEQ ID No. 1258, SEQ ID No. 115, SEQ ID No. 1151, SEQ IDNo. 151, SEQ ID No. 1259, SEQ ID No. 173, SEQ ID No. 1261, SEQ ID No.186, SEQ ID No. 194, SEQ ID No. 205, SEQ ID No. 214, SEQ ID No. 216, SEQID No. 217, SEQ ID No. 238, SEQ ID No. 1177, SEQ ID No. 280, SEQ ID No.291, SEQ ID No. 317, SEQ ID No. 327, SEQ ID No. 354, SEQ ID No. 364, SEQID No. 367, SEQ ID No. 414, SEQ ID No. 432, SEQ ID No. 1192, SEQ ID No.460, SEQ ID No. 1267, SEQ ID No. 1268, SEQ ID No. 520, SEQ ID No. 536,SEQ ID No. 1270, SEQ ID No. 576, SEQ ID No. 597, SEQ ID No. 603, SEQ IDNo. 609, SEQ ID No. 637, SEQ ID No. 1272, SEQ ID No. 652, SEQ ID No.1213, SEQ ID No. 699, SEQ ID No. 705, SEQ ID No. 706, SEQ ID No. 708,SEQ ID No. 711, SEQ ID No. 727, SEQ ID No. 1274, SEQ ID No. 800, SEQ IDNo. 814, SEQ ID No. 825, SEQ ID No. 829, SEQ ID No. 830, SEQ ID No. 831,SEQ ID No. 844, SEQ ID No. 849, SEQ ID No. 1275, SEQ ID No. 1276, SEQ IDNo. 1277, SEQ ID No. 872, SEQ ID No. 878, SEQ ID No. 880, SEQ ID No.891, SEQ ID No. 892, SEQ ID No. 1278, SEQ ID No. 1279, SEQ ID No. 1280,SEQ ID No. 941, SEQ ID No. 942, SEQ ID No. 1282, SEQ ID No. 1283, SEQ IDNo. 952, SEQ ID No. 988, SEQ ID No. 998, SEQ ID No. 1009, SEQ ID No.1285, SEQ ID No. 1235, SEQ ID No. 1028, SEQ ID No. 1056, SEQ ID No.1070, SEQ ID No. 1287, SEQ ID No. 1087, SEQ ID No. 1288, SEQ ID No.1289, SEQ ID No. 1098, SEQ ID No. 1246, SEQ ID No. 1291, SEQ ID No.1108, SEQ ID No. 1109, SEQ ID No. 1112, SEQ ID No. 1133, and one oftheir representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide involved inlipopolysaccharide (LPS) biosynthesis, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 316, SEQ ID No. 564, SEQ ID No. 610, SEQ ID No. 647, SEQ IDNo. 1211, SEQ ID No. 688, SEQ ID No. 924, and one of theirrepresentative fragments.

Preferably, the invention relates to additional LPS-related polypeptidesaccording to the invention, in that it is:

(a) a Chlamydia pneumoniae KDO (3-deoxy-D-manno-octylosonicacid)-related polypeptide or one of its representative fragments, and inthat it is chosen from the polypeptides having the following sequences:SEQ ID No. 177, SEQ ID No. 1156, SEQ ID No. 245, SEQ ID No. 767, and oneof their representative fragments;

(b) a Chlamydia pneumoniae phosphomannomutase-related polypeptide or oneof its representative fragments, and in that it is chosen from thepolypeptides having the following sequences: SEQ ID No. 74, and itsrepresentative fragment;

(c) a Chlamydia pneumoniae phosphoglucomutase-related polypeptide or oneof its representative fragments, and in that it is chosen from thepolypeptides having the following sequences: SEQ ID No. 1286, SEQ ID No.1039, and its representative fragment; and

(d) a Chlamydia pneumoniae lipid A component-related polypeptide or oneof its representative fragments, and in that it is chosen from thepolypeptides having the following sequences: SEQ ID No. 689, SEQ ID No.690, SEQ ID No. 691, SEQ ID No. 1037, and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide or one ofits representative fragments that contains an RGD sequence and is alsoan outer membrane protein, and in that it is chosen from thepolypeptides having the following sequences: SEQ ID No. 468 and itsrepresentative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide or one ofits representative fragments that contains an RGD sequence that showshomology to cds1, cds2, and copN type III virulence loci in ChlamydiaPsitacci, and in that it is chosen from the polypeptides having thefollowing sequences:

SEQ ID No. 350 and its representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide or one ofits representative fragments that is cysteine-rich and contains RGDsequence, and in that it is chosen from the polypeptides having thefollowing sequences: SEQ ID No. 1290, SEQ ID No. 6846, SEQ ID No. 6848,and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae outer membranepolypeptide that contains cysteines in their first 30 amino acids andalso contain an RGD sequence, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 105, SEQ ID No. 106, SEQ ID No. 114, SEQ ID No. 170, SEQ IDNo. 171, SEQ ID No. 1264, SEQ ID No. 268, SEQ ID No. 1265, SEQ ID No.350, SEQ ID No. 393, SEQ ID No. 394, SEQ ID No. 451, SEQ ID No. 452, SEQID No. 453, SEQ ID No. 473, SEQ ID No. 499, SEQ ID No. 515, SEQ ID No.519, SEQ ID No. 525, SEQ ID No. 526, SEQ ID No. 538, SEQ ID No. 611, SEQID No. 645, SEQ ID No. 686, SEQ ID No. 700, SEQ ID No. 746, SEQ ID No.755, SEQ ID No. 756, SEQ ID No. 757, SEQ ID No. 789, SEQ ID No. 814, SEQID No. 855, SEQ ID No. 856, SEQ ID No. 878, SEQ ID No. 957, SEQ ID No.958, SEQ ID No. 989, SEQ ID No. 1290, and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide or one ofits representative fragments that contains RGD sequences homologous toChlamydia trachomatis polypeptides containing RGD sequences, and in thatit is chosen from the polypeptides having the following sequences:

SEQ ID No. 114, SEQ ID No. 468, SEQ ID No. 755, SEQ ID No. 756, SEQ IDNo. 757, SEQ ID No. 855, SEQ ID No. 856, SEQ ID No. 905, SEQ ID No. 913,SEQ ID No. 914, SEQ ID No. 915, and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae Type III and non-TypeIII secreted polypeptide or one of its representative fragments, and inthat it is chosen from the polypeptides having the following sequences:

SEQ ID No. 25, SEQ ID No. 28, SEQ ID No. 29, SEQ ID No. 33, SEQ ID No.308, SEQ ID No. 309, SEQ ID No. 343, SEQ ID No. 344, SEQ ID No. 345, SEQID No. 367, SEQ ID No. 414, SEQ ID No. 415, SEQ ID No. 480, SEQ ID No.550, SEQ ID No. 579, SEQ ID No. 580, SEQ ID No. 581, SEQ ID No. 597, SEQID No. 699, SEQ ID No. 744, SEQ ID No. 751, SEQ ID No. 776, SEQ ID No.866, SEQ ID No. 874, SEQ ID No. 883, SEQ ID No. 884, SEQ ID No. 888, SEQID No. 891, SEQ ID No. 6845, and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae cell wall anchoredsurface polypeptide or one of its representative fragments, and in thatit is chosen from the polypeptides having the following sequences: SEQID No. 267, SEQ ID No. 271, SEQ ID No. 419, SEQ ID No. 590, SEQ ID No.932, SEQ ID No. 6844, SEQ ID No. 6847, and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, in that it is a Chlamydia pneumoniae polypeptide or one ofits representative fragments not found in Chlamydia trachomatis (BlastpP>e⁻¹⁰), and in that it is chosen from the polypeptides having thefollowing sequences:

SEQ ID No. 7, SEQ ID No. 8, SEQ ID No. 9, SEQ ID No. 16, SEQ ID No. 17,SEQ ID No. 18, SEQ ID No. 19, SEQ ID No. 20, SEQ ID No. 21, SEQ ID No.22, SEQ ID No. 1254, SEQ ID No. 23, SEQ ID No. 1255, SEQ ID No. 24, SEQID No. 1139, SEQ ID No. 1140, SEQ ID No. 46, SEQ ID No. 47, SEQ ID No.51, SEQ ID No. 60, SEQ ID No. 1256, SEQ ID No. 61, SEQ ID No. 62, SEQ IDNo. 63, SEQ ID No. 64, SEQ ID No. 1257, SEQ ID No. 65, SEQ ID No. 66,SEQ ID No. 67, SEQ ID No. 68, SEQ ID No. 1143, SEQ ID No. 1145, SEQ IDNo. 83, SEQ ID No. 84, SEQ ID No. 1146, SEQ ID No. 85, SEQ ID No. 86,SEQ ID No. 87, SEQ ID No. 1258, SEQ ID No. 116, SEQ ID No. 117, SEQ IDNo. 125, SEQ ID No. 1148, SEQ ID No. 143, SEQ ID No. 1150, SEQ ID No.1151, SEQ ID No. 144, SEQ ID No. 145, SEQ ID No. 147, SEQ ID No. 148,SEQ ID No. 149, SEQ ID No. 150, SEQ ID No. 152, SEQ ID No. 1259, SEQ IDNo. 162, SEQ ID No. 166, SEQ ID No. 1154, SEQ ID No. 167, SEQ ID No.1261, SEQ ID No. 1156, SEQ ID No. 1157, SEQ ID No. 178, SEQ ID No. 179,SEQ ID No. 1158, SEQ ID No. 182, SEQ ID No. 183, SEQ ID No. 184, SEQ IDNo. 185, SEQ ID No. 1159, SEQ ID No. 186, SEQ ID No. 1160, SEQ ID No.187, SEQ ID No. 188, SEQ ID No. 189, SEQ ID No. 190, SEQ ID No. 1161,SEQ ID No. 1162, SEQ ID No. 191, SEQ ID No. 192, SEQ ID No. 194, SEQ IDNo. 195, SEQ ID No. 1163, SEQ ID No. 196, SEQ ID No. 201, SEQ ID No.202, SEQ ID No. 209, SEQ ID No. 212, SEQ ID No. 221, SEQ ID No. 224, SEQID No. 1167, SEQ ID No. 226, SEQ ID No. 227, SEQ ID No. 228, SEQ ID No.229, SEQ ID No. 230, SEQ ID No. 231, SEQ ID No. 232, SEQ ID No. 1169,SEQ ID No. 1170, SEQ ID No. 1171, SEQ ID No. 234, SEQ ID No. 235, SEQ IDNo. 236, SEQ ID No. 1172, SEQ ID No. 243, SEQ ID No. 251, SEQ ID No.252, SEQ ID No. 1176, SEQ ID No. 253, SEQ ID No. 255, SEQ ID No. 254,SEQ ID No. 256, SEQ ID No. 1177, SEQ ID No. 1178, SEQ ID No. 262, SEQ IDNo. 263, SEQ ID No. 1264, SEQ ID No. 278, SEQ ID No. 279, SEQ ID No.1180, SEQ ID No. 280, SEQ ID No. 290, SEQ ID No. 291, SEQ ID No. 292,SEQ ID No. 296, SEQ ID No. 1181, SEQ ID No. 297, SEQ ID No. 298, SEQ IDNo. 300, SEQ ID No. 1265, SEQ ID No. 322, SEQ ID No. 324, SEQ ID No.325, SEQ ID No. 370, SEQ ID No. 1186, SEQ ID No. 371, SEQ ID No. 372,SEQ ID No. 1187, SEQ ID No. 373, SEQ ID No. 378, SEQ ID No. 1266, SEQ IDNo. 382, SEQ ID No. 383, SEQ ID No. 384, SEQ ID No. 385, SEQ ID No. 386,SEQ ID No. 1188, SEQ ID No. 1189, SEQ ID No. 391, SEQ ID No. 392, SEQ IDNo. 398, SEQ ID No. 400, SEQ ID No. 403, SEQ ID No. 1191, SEQ ID No.423, SEQ ID No. 435, SEQ ID No. 445, SEQ ID No. 450, SEQ ID No. 1193,SEQ ID No. 456, SEQ ID No. 460, SEQ ID No. 461, SEQ ID No. 465, SEQ IDNo. 1196, SEQ ID No. 471, SEQ ID No. 473, SEQ ID No. 475, SEQ ID No.481, SEQ ID No. 484, SEQ ID No. 487, SEQ ID No. 488, SEQ ID No. 489, SEQID No. 490, SEQ ID No. 491, SEQ ID No. 492, SEQ ID No. 493, SEQ ID No.494, SEQ ID No. 495, SEQ ID No. 496, SEQ ID No. 497, SEQ ID No. 498, SEQID No. 499, SEQ ID No. 502, SEQ ID No. 1267, SEQ ID No. 1268, SEQ ID No.508, SEQ ID No. 510, SEQ ID No. 509, SEQ ID No. 512, SEQ ID No. 515, SEQID No. 519, SEQ ID No. 1197, SEQ ID No. 521, SEQ ID No. 1198, SEQ ID No.522, SEQ ID No. 524, SEQ ID No. 528, SEQ ID No. 534, SEQ ID No. 537, SEQID No. 1269, SEQ ID No. 1270, SEQ ID No. 548, SEQ ID No. 551, SEQ ID No.557, SEQ ID No. 1201, SEQ ID No. 1203, SEQ ID No. 562, SEQ ID No. 566,SEQ ID No. 593, SEQ ID No. 595, SEQ ID No. 600, SEQ ID No. 1271, SEQ IDNo. 604, SEQ ID No. 611, SEQ ID No. 612, SEQ ID No. 614, SEQ ID No. 616,SEQ ID No. 625, SEQ ID No. 627, SEQ ID No. 628, SEQ ID No. 629, SEQ IDNo. 631, SEQ ID No. 641, SEQ ID No. 1272, SEQ ID No. 648, SEQ ID No.1212, SEQ ID No. 663, SEQ ID No. 685, SEQ ID No. 707, SEQ ID No. 714,SEQ ID No. 715, SEQ ID No. 716, SEQ ID No. 717, SEQ ID No. 722, SEQ IDNo. 746, SEQ ID No. 1273, SEQ ID No. 761, SEQ ID No. 764, SEQ ID No.770, SEQ ID No. 1217, SEQ ID No. 783, SEQ ID No. 1274, SEQ ID No. 803,SEQ ID No. 815, SEQ ID No. 1220, SEQ ID No. 835, SEQ ID No. 1221, SEQ IDNo. 844, SEQ ID No. 845, SEQ ID No. 846, SEQ ID No. 847, SEQ ID No. 848,SEQ ID No. 849, SEQ ID No. 850, SEQ ID No. 851, SEQ ID No. 1275, SEQ IDNo. 852, SEQ ID No. 862, SEQ ID No. 1276, SEQ ID No. 1277, SEQ ID No.873, SEQ ID No. 1223, SEQ ID No. 892, SEQ ID No. 919, SEQ ID No. 1225,SEQ ID No. 1278, SEQ ID No. 926, SEQ ID No. 1228, SEQ ID No. 1229, SEQID No. 1230, SEQ ID No. 1279, SEQ ID No. 1281, SEQ ID No. 1282, SEQ IDNo. 1283, SEQ ID No. 948, SEQ ID No. 950, SEQ ID No. 949, SEQ ID No.951, SEQ ID No. 980, SEQ ID No. 982, SEQ ID No. 1233, SEQ ID No. 999,SEQ ID No. 1000, SEQ ID No. 1001, SEQ ID No. 1002, SEQ ID No. 1008, SEQID No. 1285, SEQ ID No. 1235, SEQ ID No. 1016, SEQ ID No. 1019, SEQ IDNo. 1027, SEQ ID No. 1036, SEQ ID No. 1241, SEQ ID No. 1048, SEQ ID No.1049, SEQ ID No. 1050, SEQ ID No. 1053, SEQ ID No. 1054, SEQ ID No.1064, SEQ ID No. 1076, SEQ ID No. 1091, SEQ ID No. 1288, SEQ ID No.1093, SEQ ID No. 1289, SEQ ID No. 1101, SEQ ID No. 1103, SEQ ID No.1245, SEQ ID No. 1246, SEQ ID No. 1247, SEQ ID No. 1290, SEQ ID No.1291, SEQ ID No. 1115, SEQ ID No. 1116, SEQ ID No. 1118, SEQ ID No.1120, SEQ ID No. 1249, SEQ ID No. 1121, SEQ ID No. 1250, SEQ ID No.1126, SEQ ID No. 1251, SEQ ID No. 1127, SEQ ID No. 1128, SEQ ID No.1130, SEQ ID No. 1129, SEQ ID No. 1131, SEQ ID No. 1136, SEQ ID No.1253, SEQ ID No. 6844, SEQ ID No. 6846, SEQ ID No. 6847, SEQ ID No.6848, and one of their representative fragments

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe intermediate metabolism, in particular in the metabolism of sugarsand/or of cofactors, and in that it is chosen from the polypeptideshaving the following sequences:

SEQ ID No. 2; SEQ ID No. 55; SEQ ID No. 56; SEQ ID No. 69; SEQ ID No.75; SEQ ID No. 80; SEQ ID No. 100; SEQ ID No. 110; SEQ ID No. 114; SEQID No. 120; SEQ ID No. 121; SEQ ID No. 157; SEQ ID No. 160; SEQ ID No.161; SEQ ID No. 172; SEQ ID No. 180; SEQ ID No. 181; SEQ ID No. 198; SEQID No. 200; SEQ ID No. 225; SEQ ID No. 248; SEQ ID No. 249; SEQ ID No.276; SEQ ID No. 277; SEQ ID No. 318; SEQ ID No. 319; SEQ ID No. 320; SEQID No. 323; SEQ ID No. 331; SEQ ID No. 347; SEQ ID No. 375; SEQ ID No.376; SEQ ID No. 381; SEQ ID No. 393; SEQ ID No. 394; SEQ ID No. 395; SEQID No. 396; SEQ ID No. 409; SEQ ID No. 446; SEQ ID No. 447; SEQ ID No.448; SEQ ID No. 449; SEQ ID No. 513; SEQ ID No. 516; SEQ ID No. 571; SEQID No. 647; SEQ ID No. 662; SEQ ID No. 697; SEQ ID No. 718; SEQ ID No.793; SEQ ID No. 794; SEQ ID No. 808; SEQ ID No. 809; SEQ ID No. 838; SEQID No. 839; SEQ ID No. 840; SEQ ID No. 853; SEQ ID No. 854; SEQ ID No.918; SEQ ID No. 923; SEQ ID No. 929; SEQ ID No. 931; SEQ ID No. 938; SEQID No. 939; SEQ ID No. 958; SEQ ID No. 959; SEQ ID No. 960; SEQ ID No.966; SEQ ID No. 995; SEQ ID No. 1021; SEQ ID No. 1040; SEQ ID No. 1041;SEQ ID No. 1042; SEQ ID No. 1085; SEQ ID No. 1100; SEQ ID No. 1102; SEQID No. 1117; SEQ ID No. 1118; SEQ ID No. 1119; SEQ ID No. 1120; SEQ IDNo. 1135 and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe intermediate metabolism of nucleotides or nucleic acids, and in thatit is chosen from the polypeptides having the following sequences:

SEQ ID No. 77; SEQ ID No. 78; SEQ ID No. 138; SEQ ID No. 189; SEQ ID No.190; SEQ ID No. 233; SEQ ID No. 246; SEQ ID No. 338; SEQ ID No. 412; SEQID No. 421; SEQ ID No. 438; SEQ ID No. 607; SEQ ID No. 648; SEQ ID No.657; SEQ ID No. 740; SEQ ID No. 783; SEQ ID No. 967; SEQ ID No. 989; SEQID No. 990; SEQ ID No. 992; SEQ ID No. 1011; SEQ ID No. 1058; SEQ ID No.1059; SEQ ID No. 1073; SEQ ID No. 1074 and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe metabolism of nucleic acids, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 14; SEQ ID No. 59; SEQ ID No. 70; SEQ ID No. 71; SEQ ID No.97; SEQ ID No. 113; SEQ ID No. 137; SEQ ID No. 141; SEQ ID No. 169; SEQID No. 285; SEQ ID No. 287; SEQ ID No. 288; SEQ ID No. 313; SEQ ID No.326; SEQ ID No. 358; SEQ ID No. 411; SEQ ID No. 443; SEQ ID No. 548; SEQID No. 569; SEQ ID No. 601; SEQ ID No. 651; SEQ ID No. 654; SEQ ID No.658; SEQ ID No. 659; SEQ ID No. 664; SEQ ID No. 665; SEQ ID No. 694; SEQID No. 698; SEQ ID No. 704; SEQ ID No. 760; SEQ ID No. 762; SEQ ID No.763; SEQ ID No. 786; SEQ ID No. 787; SEQ ID No. 788; SEQ ID No. 801; SEQID No. 802; SEQ ID No. 812; SEQ ID No. 819; SEQ ID No. 822; SEQ ID No.870; SEQ ID No. 897; SEQ ID No. 898; SEQ ID No. 902; SEQ ID No. 908; SEQID No. 916; SEQ ID No. 954; SEQ ID No. 955; SEQ ID No. 961; SEQ ID No.983; SEQ ID No. 996; SEQ ID No. 1007; SEQ ID No. 1012; SEQ ID No. 1013;SEQ ID No. 1014; SEQ ID No. 1015; SEQ ID No. 1038; SEQ ID No. 1137 andone of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe metabolism of amino acids or polypeptides, and in that it is chosenfrom the polypeptides having the following sequences:

SEQ ID No. 99; SEQ ID No. 111; SEQ ID No. 127; SEQ ID No. 134; SEQ IDNo. 140; SEQ ID No. 174; SEQ ID No. 175; SEQ ID No. 176; SEQ ID No. 353;SEQ ID No. 377; SEQ ID No. 404; SEQ ID No. 523; SEQ ID No. 539; SEQ IDNo. 559; SEQ ID No. 561; SEQ ID No. 586; SEQ ID No. 598; SEQ ID No. 609;SEQ ID No. 636; SEQ ID No. 687; SEQ ID No. 700; SEQ ID No. 701; SEQ IDNo. 759; SEQ ID No. 790; SEQ ID No. 857; SEQ ID No. 861; SEQ ID No. 904;SEQ ID No. 936; SEQ ID No. 952; SEQ ID No. 962; SEQ ID No. 963; SEQ IDNo. 964; SEQ ID No. 965; SEQ ID No. 991; SEQ ID No. 1003; SEQ ID No.1004; SEQ ID No. 1005; SEQ ID No. 1018; SEQ ID No. 1067; SEQ ID No.1110; SEQ ID No. 1111; SEQ ID No. 1112; SEQ ID No. 1114; SEQ ID No.1121; SEQ ID No. 1122; SEQ ID No. 1123; SEQ ID No. 1124; SEQ ID No. 1125and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe metabolism of polypeptides, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 4; SEQ ID No. 44; SEQ ID No. 45; SEQ ID No. 48; SEQ ID No.54; SEQ ID No. 112; SEQ ID No. 130; SEQ ID No. 155; SEQ ID No. 163; SEQID No. 212; SEQ ID No. 257; SEQ ID No. 307; SEQ ID No. 343; SEQ ID No.405; SEQ ID No. 416; SEQ ID No. 458; SEQ ID No. 540; SEQ ID No. 541; SEQID No. 542; SEQ ID No. 543; SEQ ID No. 544; SEQ ID No. 560; SEQ ID No.594; SEQ ID No. 652; SEQ ID No. 699; SEQ ID No. 723; SEQ ID No. 747; SEQID No. 817; SEQ ID No. 827; SEQ ID No. 871; SEQ ID No. 909; SEQ ID No.910; SEQ ID No. 911; SEQ ID No. 912; SEQ ID No. 1023; SEQ ID No. 1051;SEQ ID No. 1052; SEQ ID No. 1081 and one of their representativefragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe metabolism of fatty acids, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 76; SEQ ID No. 284; SEQ ID No. 308; SEQ ID No. 309; SEQ IDNo. 310; SEQ ID No. 311; SEQ ID No. 312; SEQ ID No. 425; SEQ ID No. 433;SEQ ID No. 565; SEQ ID No. 688; SEQ ID No. 690; SEQ ID No. 691; SEQ IDNo. 767; SEQ ID No. 797; SEQ ID No. 894; SEQ ID No. 895; SEQ ID No. 994;SEQ ID No. 1020; SEQ ID No. 1030; SEQ ID No. 1033; SEQ ID No. 1034; SEQID No. 1046; SEQ ID No. 1047; SEQ ID No. 1057 and one of theirrepresentative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe synthesis of the wall, and in that it is chosen from thepolypeptides having the following sequences:

SEQ ID No. 49; SEQ ID No. 50; SEQ ID No. 177; SEQ ID No. 178; SEQ ID No.245; SEQ ID No. 610; SEQ ID No. 972; SEQ ID No. 974; SEQ ID No. 978; SEQID No. 1037 and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe transcription, translation and/or maturation process, and in that itis chosen from the polypeptides having the following sequences:

SEQ ID No. 90; SEQ ID No. 92; SEQ ID No. 131; SEQ ID No. 151; SEQ ID No.199; SEQ ID No. 333; SEQ ID No. 334; SEQ ID No. 336; SEQ ID No. 379; SEQID No. 589; SEQ ID No. 590; SEQ ID No. 619; SEQ ID No. 630; SEQ ID No.649; SEQ ID No. 739; SEQ ID No. 741; SEQ ID No. 806; SEQ ID No. 821; SEQID No. 843; SEQ ID No. 968; SEQ ID No. 971; SEQ ID No. 1061 and one oftheir representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniae ribosomalpolypeptide or one of its representative fragments, and in that it ischosen from the polypeptides having the following sequences:

SEQ ID No. 93; SEQ ID No. 94; SEQ ID No. 95; SEQ ID No. 136; SEQ ID No.259; SEQ ID No. 332; SEQ ID No. 348; SEQ ID No. 583; SEQ ID No. 584; SEQID No. 588; SEQ ID No. 591; SEQ ID No. 592; SEQ ID No. 663; SEQ ID No.666; SEQ ID No. 667; SEQ ID No. 669; SEQ ID No. 670; SEQ ID No. 671; SEQID No. 672; SEQ ID No. 673; SEQ ID No. 674; SEQ ID No. 675; SEQ ID No.676; SEQ ID No. 677; SEQ ID No. 678; SEQ ID No. 679; SEQ ID No. 680; SEQID No. 681; SEQ ID No. 683; SEQ ID No. 684; SEQ ID No. 738; SEQ ID No.781; SEQ ID No. 1008; SEQ ID No. 1024; SEQ ID No. 1025; SEQ ID No. 1066and one of their representative fragments.

Preferably, the invention also relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniae transportpolypeptide or one of its representative fragments, and in that it ischosen from the polypeptides having the following sequences:

SEQ ID No. 40; SEQ ID No. 41; SEQ ID No. 52; SEQ ID No. 105; SEQ ID No.106; SEQ ID No. 107; SEQ ID No. 109; SEQ ID No. 133; SEQ ID No. 210; SEQID No. 211; SEQ ID No. 214; SEQ ID No. 215; SEQ ID No. 216; SEQ ID No.217; SEQ ID No. 218; SEQ ID No. 219; SEQ ID No. 220; SEQ ID No. 223; SEQID No. 242; SEQ ID No. 260; SEQ ID No. 293; SEQ ID No. 299; SEQ ID No.366; SEQ ID No. 369; SEQ ID No. 575; SEQ ID No. 602; SEQ ID No. 638; SEQID No. 639; SEQ ID No. 640; SEQ ID No. 643; SEQ ID No. 653; SEQ ID No.702; SEQ ID No. 703; SEQ ID No. 724; SEQ ID No. 732; SEQ ID No. 855; SEQID No. 856; SEQ ID No. 901; SEQ ID No. 906; SEQ ID No. 933; SEQ ID No.942; SEQ ID No. 1043; SEQ ID No. 1086; SEQ ID No. 1105 and one of theirrepresentative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe virulence process, and in that it is chosen from the polypeptideshaving the following sequences:

SEQ ID No. 546; SEQ ID No. 550; SEQ ID No. 778; SEQ ID No. 779; SEQ IDNo. 886 and one of their representative fragments.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a Chlamydia pneumoniaepolypeptide or one of its representative fragments which is involved inthe secretory system and/or which is secreted, and in that it is chosenfrom the polypeptides having the following sequences:

SEQ ID No. 751; SEQ ID No. 874; SEQ ID No. 875; SEQ ID No. 876; SEQ IDNo. 883; SEQ ID No. 884; SEQ ID No. 885 and one of their representativefragments.

The secreted polypeptides, including the Type III and other, non-TypeIII secreted polypeptides, of the present invention, as well as thecorresponding nucleotide sequences, may be detected by techniques knownto persons skilled in the art, such as for example the techniques usingcloning combined with vectors allowing the expression of the saidpolypeptides fused to export markers such as the luc gene for luciferaseor the PhoA gene for alkaline phosphatase.

Preferably, the invention relates to a polypeptide according to theinvention, characterized in that it is a polypeptide specific toChlamydia pneumoniae or one of its representative fragments(with a BlastE value of >10⁻⁵), and in that it is chosen from the polypeptides havingthe following sequences:

SEQ ID No. 7; SEQ ID No. 8; SEQ ID No. 17; SEQ ID No. 18; SEQ ID No. 19;SEQ ID No. 20; SEQ ID No. 22; SEQ ID No. 23; SEQ ID No. 24; SEQ ID No.51; SEQ ID No. 60; SEQ ID No. 63; SEQ ID No. 65; SEQ ID No. 66; SEQ IDNo. 67; SEQ ID No. 83; SEQ ID No. 84; SEQ ID No. 86; SEQ ID No. 87; SEQID No. 125; SEQ ID No. 143; SEQ ID No. 144; SEQ ID No. 179; SEQ ID No.182; SEQ ID No. 184; SEQ ID No. 185; SEQ ID No. 187; SEQ ID No. 221; SEQID No. 252; SEQ ID No. 254; SEQ ID No. 278; SEQ ID No. 279; SEQ ID No.387; SEQ ID No. 388; SEQ ID No. 397; SEQ ID No. 1048; SEQ ID No. 1049;SEQ ID No. 1050; SEQ ID No. 1128; SEQ ID No. 1130; SEQ ID No. 1131 andone of their representative fragments.

In general, in the present invention, the functional group to which apolypeptide of the invention belongs, as well as its correspondingnucleotide sequence, may be determined either by comparative analogywith sequences already known, or by the use of standard techniques ofbiochemistry, of cytology combined with the techniques of geneticengineering such as immunoaffinity, localization by immunolabelling,differential extraction, measurement of enzymatic activity, study of theactivity inducing or repressing expression or the study of expression inE. coli.

It is clearly understood, on the one hand, that, in the presentinvention, the nucleotide sequences (ORF) and the amino acid sequences(SEQ ID No. 2 to SEQ ID No. 1291 and SEQ ID No. 6844 to SEQ ID No. 6848)which are listed by functional group, are not exhaustive within thegroup considered. Moreover, it is also clearly understood that, in thepresent invention, a nucleotide sequence (ORF) or an amino acid sequencementioned within a given functional group may also be part of anothergroup taking into account, for example, the interrelationship betweenthe groups listed. Accordingly, and as an example of thisinterrelationship, an exported and/or secreted polypeptide as well asits coding nucleotide sequence may also be involved in the Chlamydiapneumoniae virulence process by modifying the defense mechanism of theinfected host cell, or a transmembrane polypeptide or its codingnucleotide sequence is also part of the polypeptides or codingnucleotide sequences of the cellular envelope.

The subject of the present invention is also the nucleotide and/orpolypeptide sequences according to the invention, characterized in thatthe said sequences are recorded on a medium, called recording medium,whose type and nature facilitate the reading, the analysis and theexploitation of the said sequences. These media may of course alsocontain other information extracted from the present invention, such asin particular the analogies with already known sequences, such as thosementioned in Table 1 of the present description, and/or may contain, inaddition, information relating to the nucleotide and/or polypeptidesequences of other microorganisms so as to facilitate the comparativeanalysis and the exploitation of the results obtained.

Among these recording media, computer-readable media, such as magnetic,optical, electrical and hybrid media such as, for example, floppy disks,CD-ROMs or recording cassettes, are preferred in particular.

The invention also relates to nucleotide sequences which can be used asprimer or probe, characterized in that the said sequences are chosenfrom the nucleotide sequences according to the invention.

The invention relates, in addition, to the use of a nucleotide sequenceaccording to the invention, as primer or probe, for the detection and/oramplification of nucleic acid sequences.

The nucleotide sequences according to the invention may thus be used toamplify nucleotide sequences, in particular by the PCR technique(polymerase chain reaction) (Erlich, 1989; Innis et al., 1990; Rolfs etal., 1991, and White et al., 1997).

These oligodeoxyribonucleotide or oligoribonucleotide primers correspondto representative nucleotide fragments, and are advantageously at least8 nucleotides, preferably at least 12 nucleotides, 15 nucleotides andstill more preferably at least 20 nucleotides long.

Other techniques for amplifying the target nucleic acid may beadvantageously used as alternatives to PCR.

The nucleotide sequences of the invention, in particular the primersaccording to the invention, may also be used in other methods foramplifying a target nucleic acid, such as:

-   the TAS (Transcription-based Amplification System) technique    described by Kwoh et al. in 1989;-   the 3SR (Self-Sustained Sequence Replication) technique described by    Guatelli et al. in 1990;-   the NASBA (Nucleic Acid Sequence Based Amplification) technique    described by Kievitis et al. in 1991;-   the SDA (Strand Displacement Amplification) technique (Walker et    al., 1992);-   the TMA (Transcription Mediated Amplification) technique.

The polynucleotides of the invention may also be used in techniques foramplifying or for modifying the nucleic acid serving as probe, such as:

-   the LCR (Ligase Chain Reaction) technique described by Landegren et    al. in 1988 and perfected by Barany et al. in 1991, which uses a    thermostable ligase;-   the RCR (Repair Chain Reaction) technique described by Segev in    1992;-   the CPR (Cycling Probe Reaction) technique described by Duck et al.    in 1990;-   the Q-beta-replicase amplification technique described by Miele et    al. in 1983 and perfected in particular by Chu et al. in 1986,    Lizardi et al. in 1988, and then by Burg et al. as well as by Stone    et al. in 1996.

The invention also relates to the nucleotide sequences of fragmentswhich can be obtained by amplification with the aid of at least oneprimer according to the invention. The present invention encompassesboth hybridization probes and primers. In general, the complementaryprobes should be of a length sufficient to form a stable hybrid complexwith the target sequences. Primers, while complementary to the targetsequences need not form stable hybridization complexes with the targetsequences alone. Rather, primers form stable complexes with the targetsequences in the presence of polymerase to permit extension of theprimer.

In the case where the target polynucleotide to be detected is possiblyan RNA, for example an mRNA, it will be possible to use, prior to theuse of an amplification reaction with the aid of at least one primeraccording to the invention or to the use of a method of detection withthe aid of at least one probe of the invention, a reversetranscriptase-type enzyme so as to obtain a cDNA from the RNA containedin the biological sample. The cDNA obtained will then serve as targetfor the primer(s) or the probe(s) used in the amplification or detectionmethod according to the invention.

The detection probe will be chosen so that it hybridizes with the targetsequence or the amplicon generated from the target sequence. Such adetection probe will advantageously have as sequence a sequence of atleast 12 nucleotides, in particular of at least 20 nucleotides, andpreferably at least 100 nucleotides.

The invention also comprises the nucleotide sequences which can be usedas probe or primer according to the invention, characterized in thatthey are labelled with a radioactive compound or with a nonradioactivecompound.

The nonlabelled nucleotide sequences may be used directly as probes orprimers; however, the sequences are generally labelled with aradioactive element (³²P, ³⁵S, ³H, ¹²⁵I) or with a nonradioactivemolecule (biotin, acetylaminofluorene, digoxigenin,5-bromo-deoxyuridine, fluorescein) so as to obtain probes which can beused in numerous applications.

Examples of nonradioactive labelling of nucleotide sequences aredescribed, for example, in French patent No. 78,10975 or by Urdea et al.or by Sanchez-Pescador et al. in 1988.

In the latter case, one of the labelling methods described in patentsFR-2 422 956 and FR-2 518 755 may also be used.

The invention also relates to the nucleotide sequences of fragmentswhich can be obtained by hybridization with the aid of at least oneprobe according to the invention.

The hybridization technique may be performed in various ways (Matthewset al., 1988). The most common method consists in immobilizing thenucleic acid extracted from Chlamydia pneumoniae cells on a support(such as nitrocellulose, nylon, polystyrene) and in incubating, underwell-defined conditions, the target nucleic acid immobilized with theprobe. After hybridization, the excess probe is removed and the hybridmolecules formed are detected by the appropriate method (measurement ofthe radioactivity, of the fluorescence or of the enzymatic activitylinked to the probe).

The invention also comprises the nucleotide sequences according to theinvention, characterized in that they are covalently or noncovalentlyimmobilized on a support.

According to another advantageous embodiment of the nucleic sequencesaccording to the invention, the latter may be used immobilized on asupport and may thus serve to capture, through specific hybridization,the target nucleic acid obtained from the biological sample to betested. If necessary, the solid support is separated from the sample andthe hybridization complex formed between the so-called capture probe andthe target nucleic acid is then detected by means of a second probe,called detection probe, labelled with an easily detectable element.

The nucleotide sequences according to the invention may also be used innew analytical systems, DNA chips, which allow sequencing, the study ofmutations and of the expression of genes, and which are currently ofinterest given their very small size and their high capacity in terms ofnumber of analyses.

The principle of the operation of these chips is based on molecularprobes, most often oligonucleotides, which are attached onto aminiaturized surface, generally of the order of a few squarecentimetres. During an analysis, a sample containing fragments of atarget nucleic acid to be analysed, for example DNA or RNA labelled, forexample, after amplification, is deposited onto the DNA chip in whichthe support has been coated beforehand with probes. Bringing thelabelled target sequences into contact with the probes leads to theformation, through hybridization, of a duplex according to the rule ofpairing defined by J. D. Watson and F. Crick. After a washing step,analysis of the surface of the chip allows the effective hybridizationsto be located by means of the signals emitted by the labels tagging thetarget. A hybridization fingerprint results from this analysis which, byappropriate computer processing, will make it possible to determineinformation such as the presence of specific fragments in the sample,the determination of sequences and the presence of mutations.

The chip consists of a multitude of molecular probes, preciselyorganized or arrayed on a solid support whose surface is miniaturized.It is at the centre of a system where other elements (imaging system,microcomputer) allow the acquisition and interpretation of ahybridization fingerprint.

The hybridization supports are provided in the form of flat or poroussurfaces (pierced with wells) composed of various materials. The choiceof a support is determined by its physicochemical properties, or moreprecisely, by the relationship between the latter and the conditionsunder which the support will be placed during the synthesis or theattachment of the probes or during the use of the chip. It is thereforenecessary, before considering the use of a particular support (R. S.Matson et al., 1994), to consider characteristics such as its stabilityto pH, its physical strength, its reactivity and its chemical stabilityas well as its capacity to nonspecifically bind nucleic acids. Materialssuch as glass, silicon and polymers are commonly used. Their surface is,in a first step, called “functionalization”, made reactive towards thegroups which it is desired to attach thereon. After thefunctionalization, so-called spacer molecules are grafted onto theactivated surface. Used as intermediates between the surface and theprobe, these molecules of variable size render unimportant the surfaceproperties of the supports, which often prove to be problematic for thesynthesis or the attachment of the probes and for the hybridization.

Among the hybridization supports, there may be mentioned glass which isused, for example, in the method of in situ synthesis ofoligonucleotides by photochemical addressing developed by the companyAffymetrix (E. L. Sheldon, 1993), the glass surface being activated bysilane. Genosensor Consortium (P. Mérel, 1994) also uses glass slidescarrying wells 3 mm apart, this support being activated withepoxysilane.

Polymers or silicon may also be mentioned among these hybridizationsupports. For example, the Andrein Mirzabekov team has developed a chipconsisting of polyacrylamide squares polymerized on a silanized glasssurface (G. Yershov et al., 1996). Several teams use silicon, inparticular the IFOS laboratory of Ecole Centrale of Lyon which uses asilicon semiconductor substrate which is p-doped by introducing it intoits crystalline structure atoms whose valency is different from that ofsilicon. Various types of metals, in particular gold and platinum, mayalso be used as support (Genosensor Consortium (K. Beattie et al.,1993)).

The probes according to the invention may be synthesized directly insitu on the supports of the DNA chips. This in situ synthesis may becarried out by photochemical addressing (developed by the companyAffymax (Amsterdam, Holland) and exploited industrially by itssubsidiary Affymetrix (United States)) or based on the VLSIPS (verylarge scale immobilized polymer synthesis) technology (S. P. A. Fodor etal., 1991) which is based on a method of photochemically directedcombinatory synthesis and the principle of which combines solid-phasechemistry, the use of photolabile protecting groups andphotolithography.

The probes according to the invention may be attached to the DNA chipsin various ways such as electrochemical addressing, automated addressingor the use of probe printers (T. Livache et al., 1994; G. Yershov etal., 1996; J. Derisi et al., 1996, and S. Borman, 1996).

The revealing of the hybridization between the probes of the invention,deposited or synthesized in situ on the supports of the DNA chips, andthe sample to be analysed, may be determined, for example, bymeasurement of fluorescent signals, by radioactive counting or byelectronic detection.

The use of fluorescent molecules such as fluorescein constitutes themost common method of labelling the samples. It allows direct orindirect revealing of the hybridization and allows the use of variousfluorochromes.

Affymetrix currently provides an apparatus or a scanner designed to readits GENE CHIP chips. It makes it possible to detect the hybridizationsby scanning the surface of the chip in confocal microscopy (R. J.Lipshutz et al., 1995). Other methods of detecting fluorescent signalshave been tested: coupling of an epifluorescence microscope and a CCDcamera (G. Yershov et al., 1996), the use of an optical fibre collectingsystem (E. L. Sheldon, 1993). A conventional method consists in carryingout an end labelling, with phosphorus 32, of the target sequences, bymeans of an appropriate apparatus, the Phosphorimager (marketed byMolecular Dynamics). The electronic detection is based on the principlethat the hybridization of two nucleic acid molecules is accompanied byphysical phenomena which can be quantified under certain conditions(system developed by Ecole Centrale of Lyon and called GEN-FET (GENfield effect transistor)). Genosensor Consortium and the company BeckmanInstruments who are developing an electronic chip or PERMITTIVITY CHIPSmay also be mentioned (K. Beattie et al., 1993).

The nucleotide sequences according to the invention may thus be used inDNA chips to carry out the analysis of mutations. This analysis is basedon the production of chips capable of analysing each base of anucleotide sequence according to the invention.

The nucleotide sequences according to the invention may also be used inDNA chips to carry out the analysis of the expression of the Chlamydiapneumoniae genes. This analysis of the expression of Chlamydiapneumoniae genes is based on the use of chips where probes of theinvention, chosen for their specificity to characterize a given gene,are present (D. J. Lockhart et al., 1996; D. D. Shoemaker et al., 1996).For the methods of analysis of gene expression using the DNA chips,reference may, for example, be made to the methods described by D. J.Lockhart et al. (1996) and Sosnowsky et al. (1997) for the synthesis ofprobes in situ or for the addressing and the attachment of previouslysynthesized probes. The target sequences to be analysed are labelled andin general fragmented into sequences of about 50 to 100 nucleotidesbefore being hybridized onto the chip. After washing as described, forexample, by D. J. Lockhart et al. (1996) and application of differentelectric fields (Sosnowsky et al., 1997), the labelled compounds aredetected and quantified, the hybridizations being carried out at leastin duplicate. Comparative analyses of the signal intensities obtainedwith respect to the same probe for different samples and/or fordifferent probes with the same sample, determine the differentialexpression of RNA or of DNA derived from the sample.

The nucleotide sequences according to the invention may, in addition, beused in DNA chips where other nucleotide probes specific for othermicroorganisms are also present, and may allow the carrying out of aserial test allowing rapid identification of the presence of amicroorganism in a sample.

Accordingly, the subject of the invention is also the nucleotidesequences according to the invention, characterized in that they areimmobilized on a support of a DNA chip.

The DNA chips, characterized in that they contain at least onenucleotide sequence according to the invention, immobilized on thesupport of the said chip, also form part of the invention.

The said chips will preferably contain several probes or nucleotidesequences of the invention of different length and/or corresponding todifferent genes so as to identify, with greater certainty, thespecificity of the target sequences or the desired mutation in thesample to be analysed.

Accordingly, the analyses carried out by means of primers and/or probesaccording to the invention, immobilized on supports such as DNA chips,will make it possible, for example, to identify, in samples, mutationslinked to variations such as intraspecies variations. These variationsmay be correlated or associated with pathologies specific to the variantidentified and will make it possible to select the appropriatetreatment.

The invention thus comprises a DNA chip according to the invention,characterized in that it contains, in addition, at least one nucleotidesequence of a microorganism different from Chlamydia pneumoniae,immobilized on the support of the said chip; preferably, the differentmicroorganism will be chosen from an associated microorganism, abacterium of the Chlamydia family, and a variant of the speciesChlamydia pneumoniae.

Another subject of the present invention is a vector for the cloningand/or the expression of a sequence, characterized in that it contains anucleotide sequence according to the invention. Among the said vectorsaccording to the invention, the vectors containing a nucleotide sequenceencoding a polypeptide of the cellular, preferably outer, envelope ofChlamydia pneumoniae or one of its representative fragments, arepreferred. In a specific embodiment, the vectors contain a nucleotidesequence encoding a Chlamydia pneumoniae secreted polypeptide or one ofits representative fragments or encoding a transport polypeptide, asurface exposed polypeptide, a lipoprotein or one of its representativefragments, a polypeptide involved in lipopolysaccharide (LPS)biosynthesis, a Type III and non-Type III secreted polypeptide, apolypeptide containing RGD attachment sites, a cell wall anchoredsurface polypeptide, a polypeptide not found in Chlamydia trachomatis, aribosomal polypeptide or a polypeptide involved in secretion,transcription, translation, maturation of proteins, a polypeptideinvolved in the synthesis of the wall, a polypeptide involved in thevirulence, a polypeptide involved in the intermediate metabolism, inparticular in the metabolism of sugars and/or of cofactors, apolypeptide involved in the metabolism of nucleotides, of amino acids,of nucleic acids or of fatty acids of Chlamydia pneumoniae or one oftheir representative fragments, or a polypeptide specific to Chlamydiapneumoniae.

According to the invention, the vectors comprise the elements necessaryto allow the expression and/or the secretion of the said nucleotidesequences in a given host cell, and form part of the invention. Thevector should, in this case, comprise a promoter, signals for initiationand for termination of translation, as well as appropriate regions forregulation of transcription. It should be capable of being stablymaintained in the host cell and may optionally possess particularsignals specifying the secretion of the translated protein. Thesedifferent elements are chosen according to the host cell used. To thiseffect, the nucleotide sequences according to the invention may beinserted into autonomously-replicating vectors within the chosen host,or integrative vectors in the chosen host.

Any of the standard methods known to those skilled in the art for theinsertion of DNA fragments into a vector may be used to constructexpression vectors containing a chimeric gene consisting of appropriatetranscriptional/translational control signals and the protein codingsequences. These methods may include in vitro recombinant DNA andsynthetic techniques and in vivo recombinants (genetic recombination).

Expression of a polypeptide, peptide or derivative, or analogs thereofencoded by a polynucleotide sequence in SEQ ID No. 1 or ORFs containedwithin SEQ ID No. 1 may be regulated by a second nucleic acid sequenceso that the protein or peptide is expressed in a host transformed withthe recombinant DNA molecule. For example, expression of a protein orpeptide may be controlled by any promoter/enhancer element known in theart. Promoters which may be used to control expression include, but arenot limited to, the CMV promoter, the SV40 early promoter region(Bernoist and Chambon, 1981, Nature 290:304–310), the promoter containedin the 3′ long terminal repeat of Rous sarcoma virus (Yamamoto, et al.,1980, Cell 22:787–797), the herpes thymidine kinase promoter (Wagner etal., 1981, Proc. Natl. Acad. Sci. U.S.A. 78:1441–1445), the regulatorysequences of the metallothionein gene (Brinster et al., 1982, Nature296:39–42); prokaryotic expression vectors such as the ∃-lactamasepromoter (Villa-Kamaroff, et al., 1978, Proc. Natl. Acad. Sci. U.S.A.75:3727–3731), or the tac promoter (DeBoer, et al., 1983, Proc. Natl.Acad. Sci. U.S.A. 80:21–25); see also “Useful proteins from recombinantbacteria” in Scientific American, 1980, 242:74–94; plant expressionvectors comprising the nopaline synthetase promoter region(Herrera-Estrella et al., 1983, Nature 303:209–213) or the cauliflowermosaic virus 35S RNA promoter (Gardner, et al., 1981, Nucl. Acids Res.9:2871), and the promoter of the photosynthetic enzyme ribulosebiphosphate carboxylase (Herrera-Estrella et al., 1984, Nature310:115–120); promoter elements from yeast or other fungi such as theGal 4 promoter, the ADC (alcohol dehydrogenase) promoter, PGK(phosphoglycerol kinase) promoter, alkaline phosphatase promoter, andthe following animal transcriptional control regions, which exhibittissue specificity and have been utilized in transgenic animals:elastase I gene control region which is active in pancreatic acinarcells (Swift et al., 1984, Cell 38:639–646; Ornitz et al., 1986, ColdSpring Harbor Symp. Quant. Biol. 50:399–409; MacDonald, 1987, Hepatology7:425–515); insulin gene control region which is active in pancreaticbeta cells (Hanahan, 1985, Nature 315:115–122), immunoglobulin genecontrol region which is active in lymphoid cells (Grosschedl et al.,1984, Cell 38:647–658; Adames et al., 1985, Nature 318:533–538;Alexander et al., 1987, Mol. Cell. Biol. 7:1436–1444), mouse mammarytumor virus control region which is active in testicular, breast,lymphoid and mast cells (Leder et al., 1986, Cell 45:485–495), albumingene control region which is active in liver (Pinkert et al., 1987,Genes and Devel. 1:268–276), alpha-fetoprotein gene control region whichis active in liver (Krumlauf et al., 1985, Mol. Cell. Biol. 5:1639–1648;Hammer et al., 1987, Science 235:53–58; alpha 1-antitrypsin gene controlregion which is active in the liver (Kelsey et al., 1987, Genes andDevel. 1:161–171), beta-globin gene control region which is active inmyeloid cells (Mogram et al., 1985, Nature 315:338–340; Kollias et al.,1986, Cell 46:89–94; myelin basic protein gene control region which isactive in oligodendrocyte cells in the brain (Readhead et al., 1987,Cell 48:703–712); myosin light chain-2 gene control region which isactive in skeletal muscle (Sani, 1985, Nature 314:283–286), andgonadotropic releasing hormone gene control region which is active inthe hypothalamus (Mason et al., 1986, Science 234:1372–1378).

The vectors according to the invention are, for example, vectors ofplasmid or viral origin. In a specific embodiment, a vector is used thatcomprises a promoter operably linked to a protein or peptide-encoding anucleic acid sequence in SEQ ID No. 1, or ORFs contained within SEQ IDNo. 1, one or more origins of replication, and, optionally, one or moreselectable markers (e.g., an antibiotic resistance gene). Expressionvectors comprise regulatory sequences that control gene expression,including gene expression in a desired host cell. Preferred vectors forthe expression of the polypeptides of the invention include the pET-typeplasmid vectors (Promega) or pBAD plasmid vectors (Invitrogen).Furthermore, the vectors according to the invention are useful fortransforming host cells so as to clone or express the nucleotidesequences of the invention.

Expression can also be achieved using targeted homologous recombinationto activate Chlamydia pneumoniae genes present in the cloned genomicDNA. A heterologous regulatory element may be inserted into a stablecell line or cloned microorganism, such that it is operatively linkedwith an endogenous Chlamydia pneumoniae gene present in the clonedgenome, using techniques, such as targeted homologous recombination,which are well known to those of skill in the art (See, e.g., Chappel,U.S. Pat. No. 4,215,051 and Skoultchi, WO 91/06667 each of which isincorporated herein in its entirety).

Expression vector/host cell systems containing inserts of polynucleotidesequences in SEQ ID No. 1 or ORFs within SEQ ID No. 1, which encodepolypeptides, peptides or derivatives, or analogs thereof, can beidentified by three general approaches: (a) nucleic acid hybridization,(b) presence or absence of “marker” gene functions, and (c) expressionof inserted sequences. In the first approach, the presence of apolynucleotide sequence inserted in an expression vector can be detectedby nucleic acid hybridization using probes comprising sequences that arehomologous to an inserted polynucleotide sequence. In the secondapproach, the recombinant vector/host system can be identified andselected based upon the presence or absence of certain “marker” genefunctions (e.g., thymidine kinase activity, resistance to antibiotics,transformation phenotype, occlusion body formation in baculovirus, etc.)caused by the insertion of a polynucleotide sequence in the vector. Forexample, if the polynucleotide sequence in SEQ ID No. 1 or ORFs withinSEQ ID No. 1 is inserted within the marker gene sequence of the vector,recombinants containing the insert can be identified by the absence ofthe marker gene function. In the third approach, recombinant expressionvectors can be identified by assaying the product of the polynucleotidesequence expressed by the recombinant. Such assays can be based, forexample, on the physical or functional properties of the expressedpolypeptide in in vitro assay systems, e.g., binding with antibody,promotion of cell proliferation.

Once a particular recombinant DNA molecule is identified and isolated,several methods known in the art may be used to propagate it. The clonesidentified may be introduced into an appropriate host cell by standardmethods, such as for example lipofection, electroporation, and heatshock. Once a suitable host system and growth conditions areestablished, recombinant expression vectors can be propagated andprepared in quantity.

The invention also encompasses the host cells transformed by a vectoraccording to the invention. These cells may be obtained by introducinginto host cells a nucleotide sequence inserted into a vector as definedabove, and then culturing the said cells under conditions allowing thereplication and/or the expression of the transfected nucleotidesequence.

The host cell may be chosen from eukaryotic or prokaryotic systems, suchas for example bacterial cells (Olins and Lee, 1993), but also yeastcells (Buckholz, 1993), as well as animal cells, in particular culturesof mammalian cells (Edwards and Aruffo, 1993), and in particular Chinesehamster ovary (CHO) cells, but also insect cells in which methods usingbaculoviruses for example may be used (Luckow, 1993).

Furthermore, a host cell strain may be chosen which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Expression from certainpromoters can be elevated in the presence of certain inducers; thus,expression of the genetically engineered polypeptide may be controlled.Furthermore, different host cells have characteristic and specificmechanisms for the translational and post-translational processing andmodification (e.g., glycosylation, phosphorylation) of proteins.Appropriate cell lines or host systems can be chosen to ensure thedesired modification and processing of the foreign protein expressed.For example, expression in a bacterial system can be used to produce anunglycosylated core protein product. Expression in yeast will produce aglycosylated product. Expression in mammalian cells can be used toensure “native” glycosylation of a heterologous protein. Furthermore,different vector/host expression systems may effect processing reactionsto different extents.

A preferred host cell for the expression of the proteins of theinvention consists of prokaryotic cells, such as Gram⁻ bacteria. Afurther preferred host cell according to the invention is a bacteriumbelonging to the Chlamydia family, more preferably belonging to thespecies Chlamydia pneumoniae or chosen from a microorganism associatedwith the species Chlamydia pneumoniae.

In other specific embodiments, the polypeptides, peptides orderivatives, or analogs thereof may be expressed as a fusion, orchimeric protein product (comprising the protein, fragment, analog, orderivative joined via a peptide bond to a heterologous protein sequence(of a different protein)). Such a chimeric product can be made byligating the appropriate nucleic acid sequences encoding the desiredamino acid sequences to each other by methods known in the art, in theproper coding frame, and expressing the chimeric product by methodscommonly known in the art. Alternatively, such a chimeric product may bemade by protein synthetic techniques, e.g., by use of a peptidesynthesizer.

Genomic sequences can be cloned and expressed as translational geneproducts (i.e., peptides, polypeptides, and proteins) or transcriptionalgene products (i.e., antisense and ribozymes).

The invention further relates to the intracellular production of anantisense nucleic acid sequence of SEQ ID No. 1 by transcription from anexogenous sequence. For example, a vector can be introduced in vivo suchthat it is taken up by a cell, within which cell the vector or a portionthereof is transcribed, producing an antisense nucleic acid (RNA) of theinvention. Such a vector would contain a sequence encoding an antisensenucleic acid. Such a vector can remain episomal or become chromosomallyintegrated, as long as it can be transcribed to produce the desiredantisense RNA. Such vectors can be constructed by recombinant DNAtechnology methods standard in the art. Vectors can be plasmid, viral,or others known in the art, used for replication and expression inmammalian cells. Expression of the sequence encoding the an antisenseRNA can be by any promoter known in the art to act in mammalian,preferably human, cells. Such promoters can be inducible orconstitutive. Such promoters include but are not limited to: the CMVpromoter, the SV40 early promoter region (Bernoist and Chambon, 1981,Nature 290:304–310), the promoter contained in the 3N long terminalrepeat of Rous sarcoma virus (Yamamoto et al., 1980, Cell 22:787–797),the herpes thymidine kinase promoter (Wagner et al., 1981, Proc. Natl.Acad. Sci. U.S.A. 78:1441–1445), the regulatory sequences of themetallothionein gene (Brinster et al., 1982, Nature 296:39–42), etc.

In a specific embodiment, the antisense oligonucleotide comprisescatalytic RNA, or a ribozyme (see, e.g., PCT International PublicationWO 90/11364, published Oct. 4, 1990; Sarver et al., 1990, Science247:1222–1225). In another embodiment, the oligonucleotide is a2N-0-methylribonucleotide (Inoue et al., 1987, Nucl. Acids Res.15:6131–6148), or a chimeric RNA-DNA analog (Inoue et al., 1987, FEBSLett. 215:327–330).

In another embodiment, the antisense nucleic acids of the inventioncomprise a sequence complementary to at least a portion of an RNAtranscript of a polynucleotide sequence in SEQ ID No. 1. However,absolute complementarity, although preferred, is not required. Asequence “complementary to at least a portion of an RNA,” as referred toherein, means a sequence having sufficient complementarity to be able tohybridize with the RNA, forming a stable duplex; in the case ofdouble-stranded antisense nucleic acid sequence, a single strand of theduplex DNA may thus be tested, or triplex formation may be assayed. Theability to hybridize will depend on both the degree of complementarityand the length of the antisense nucleic acid. Generally, the longer thehybridizing nucleic acid, the more base mismatches with an RNAtranscribed from SEQ ID No. 1 may contain and still form a stable duplex(or triplex, as the case may be). One skilled in the art can ascertain atolerable degree of mismatch by use of standard procedures to determinethe melting point of the hybridized complex.

The invention also relates to the animals, except humans, comprising oneof the above-described transformed cells according to the invention.

The production of transgenic animals according to the inventionoverexpressing one or more of the Chlamydia pneumoniae genes will bepreferably carried out on rats, mice or rabbits according to methodswell known to persons skilled in the art such as viral or nonviraltransfections. The transgenic animals overexpressing one or more of thesaid genes may be obtained by transfection of multiple copies of thesaid genes under the control of a powerful promoter of a ubiquitousnature, or which is selective for one type of tissue. The transgenicanimals may also be obtained by homologous recombination on embryonicstem cells, transfer of these stem cells to embryos, selection of thechimeras affected at the level of the reproductive lines, and growth ofthe said chimeras.

The transformed cells as well as the transgenic animals according to theinvention can be used in methods of preparing the recombinantpolypeptide.

It is now possible to produce recombinant polypeptides in a relativelylarge quantity by genetic engineering using the cells transformed withexpression vectors according to the invention or using transgenicanimals according to the invention.

The methods of preparing a polypeptide of the invention in recombinantform, characterized in that they use a vector and/or a cell, transformedwith a vector according to the invention and/or a transgenic animalcomprising one of the said transformed cells according to the invention,are themselves included in the present invention.

Among the said methods of preparing a polypeptide of the invention inrecombinant form, the methods of preparation using a vector, and/or acell transformed with the said vector and/or a transgenic animalcomprising one of the said transformed cells, containing a nucleotidesequence encoding a polypeptide of the cellular envelope of Chlamydiapneumoniae or one of its representative fragments, more preferablyencoding a polypeptide of the outer cellular envelope of Chlamydiapneumoniae or one of its fragment, are preferred.

Among the said methods of preparing a polypeptide of the invention inrecombinant form, the methods of preparation using a vector, and/or acell transformed with the said vector and/or a transgenic animalcomprising one of the said transformed cells, containing a nucleotidesequence encoding a Chlamydia pneumoniae secreted polypeptide or one ofits representative fragments or encoding a transport polypeptide, asurface exposed polypeptide, a lipoprotein or one of its representativefragments, a polypeptide involved in lipopolysaccharide biosynthesis, aType III or other secreted polypeptide, a polypeptide containing RGDattachment sites, a cell wall anchored surface polypeptide, apolypeptide not found in Chlamydia trachomatis, a ribosomal polypeptideor a polypeptide involved in secretion, transcription, translation,maturation of proteins, a polypeptide involved in the synthesis of thewall, a polypeptide involved in the virulence, a polypeptide involved inthe intermediate metabolism, in particular in the metabolism of sugarsand/or of cofactors, a polypeptide involved in the metabolism ofnucleotides, of amino acids, of nucleic acids or of fatty acids ofChlamydia pneumoniae or one of their representative fragments, or apolypeptide specific to Chlamydia pneumoniae, are also preferred.

The recombinant polypeptides obtained as indicated above may be providedeither in glycosylated or non-glycosylated form and may or may not havethe natural tertiary structure.

A preferred variant consists in producing a recombinant polypeptidefused to a “carrier” protein (chimeric protein). The advantage of thissystem is that it allows a stabilization and a reduction in proteolysisof the recombinant product, an increase in solubility duringrenaturation in vitro and/or a simplification of purification when thefusion partner has affinity for a specific ligand.

More particularly, the invention relates to a method of preparing apolypeptide of the invention comprising the following steps:

-   a) culture of the transformed cells under conditions allowing the    expression of a recombinant polypeptide having a nucleic acid    sequence according to the invention;-   b) where appropriate, recovery of the said recombinant polypeptide.

When the method of preparing a polypeptide of the invention uses atransgenic animal according to the invention, the recombinantpolypeptide is then extracted from the said animal.

The subject of the invention is also a polypeptide capable of beingobtained by a method of the invention as described above.

The invention also comprises a method of preparing a syntheticpolypeptide, characterized in that it uses an amino acid sequence ofpolypeptides according to the invention.

The invention also relates to a synthetic polypeptide obtained by amethod according to the invention.

Polypeptides according to the invention may also be prepared byconventional techniques in the field of peptide synthesis underconditions suitable to produce the polypeptides encoded by thepolynucleotide of the invention. This synthesis may be carried out inand recovered from a homogeneous solution or on a solid phase.

For example, the synthesis technique in a homogeneous solution describedby Houbenweyl in 1974 may be used.

This method of synthesis consists in successively condensing, in pairs,the successive amino acids in the required order, or in condensing aminoacids and fragments previously formed and already containing severalamino acids in the appropriate order, or alternatively several fragmentsthus previously prepared, it being understood that care will have beentaken to protect beforehand all the reactive functional groups carriedby these amino acids or fragments, with the exception of the aminefunctional groups of one and the carboxyl functional groups of the otheror vice versa, which should normally take part in the formation of thepeptide bonds, in particular after activation of the carboxyl functionalgroup, according to methods well known in peptide synthesis.

According to another preferred technique of the invention, the onedescribed by Merrifield is used.

To manufacture a peptide chain according to the Merrifield method, ahighly porous polymer resin is used, onto which the first C-terminalamino acid of the chain is attached. This amino acid is attached onto aresin via its carboxyl group and its amine functional group isprotected. The amino acids which will constitute the peptide chain arethus attached, one after another, onto the amine group, each timedeprotected beforehand, of the portion of the peptide chain alreadyformed, and which is attached to the resin. When the entire peptidechain desired is formed, the protecting groups are removed from thevarious amino acids constituting the peptide chain and the peptide isdetached from the resin with the aid of an acid.

The invention relates, in addition, to hybrid (fusion) polypeptideshaving at least one polypeptide or one of its representative fragmentsaccording to the invention, and a sequence of a polypeptide capable ofeliciting an immune response in humans or animals.

Advantageously, the antigenic determinant is such that it is capable ofeliciting a humoral and/or cellular response. An antigenic determinantmay be identified by screening expression libraries of the Chlamydiapneumoniae genome with antibodies contained in the serum of patientsinfected with a bacterium belonging to the species Chlamydia pneumoniae.An antigenic determinant may comprise a polypeptide or one of itsrepresentative fragments according to the invention, in glycosylatedform, used in order to obtain immunogenic compositions capable ofinducing the synthesis of antibodies directed against multiple epitopes.The said polypeptides or their glycosylated fragments also form part ofthe invention.

These hybrid molecules may consist, in part, of a carrier molecule forpolypeptides or for their representative fragments according to theinvention, combined with a portion which may be immunogenic, inparticular an epitope of the diphtheria toxin, the tetanus toxin, ahepatitis B virus surface antigen (patent FR 79 21811), thepoliomyelitis virus VP1 antigen or any other viral or bacterial toxin orantigen.

The methods of synthesizing the hybrid molecules include the methodsused in genetic engineering to construct hybrid nucleotide sequencesencoding the desired polypeptide sequences. Reference may beadvantageously made, for example, to the technique for producing genesencoding fusion proteins described by Minton in 1984.

The said hybrid nucleotide sequences encoding a hybrid polypeptide aswell as the hybrid polypeptides according to the invention,characterized in that they are recombinant polypeptides obtained by theexpression of the said hybrid nucleotide sequences, also form part ofthe invention.

The invention also comprises the vectors characterized in that theycontain one of the said hybrid nucleotide sequences. The host cellstransformed by the said vectors, the transgenic animals comprising oneof the said transformed cells as well as the methods of preparingrecombinant polypeptides using the said vectors, the said transformedcells and/or the said transgenic animals of course also form part of theinvention.

The polypeptides according to the invention, the antibodies according tothe invention described below and the nucleotide sequences according tothe invention may advantageously be used in in vitro and/or in vivomethods for the detection and/or the identification of bacteriabelonging to the species Chlamydia pneumoniae, in a biological sample(biological tissue or fluid) which is likely to contain them. Thesemethods, depending on the specificity of the polypeptides, of theantibodies and of the nucleotide sequences according to the inventionwhich will be used, may in particular detect and/or identify thebacterial variants belonging to the species Chlamydia pneumoniae as wellas the associated microorganisms capable of being detected by thepolypeptides, the antibodies and the nucleotide sequences according tothe invention which will be chosen. It may, for example, be advantageousto choose a polypeptide, an antibody or a nucleotide sequence accordingto the invention, which is capable of detecting any bacterium of theChlamydia family by choosing a polypeptide, an antibody and/or anucleotide sequence according to the invention which is specific to thefamily or, on the contrary, it will be most particularly advantageous totarget a variant of the species Chlamydia pneumoniae, which isresponsible, for example, for the induction or the worsening ofpathologies specific to the targeted variant, by choosing a polypeptide,an antibody and/or a nucleotide sequence according to the inventionwhich is specific to the said variant.

The polypeptides according to the invention may advantageously be usedin a method for the detection and/or the identification of bacteriabelonging to the species Chlamydia pneumoniae or to an associatedmicroorganism, in a biological sample (biological tissue or fluid) whichis likely to contain them, characterized in that it comprises thefollowing steps:

-   a) bringing this biological sample into contact with a polypeptide    or one of its representative fragments according to the invention    (under conditions allowing an immunological reaction between the    said polypeptide and the antibodies which may be present in the    biological sample);-   b) detecting the antigen-antibody complexes which may be formed.

Preferably, the biological sample consists of a fluid, for example ahuman or animal serum, blood or biopsies.

Any conventional procedure may be used to carry out such a detection ofthe antigen-antibody complexes which may be formed.

By way of example, a preferred method uses immunoenzymatic proceduresbased on the ELISA technique, immunofluorescence procedures orradioimmunological procedures (RIA), and the like.

Accordingly, the invention also relates to the polypeptides according tothe invention, labelled with the aid of a suitable label such as a labelof the enzymatic, fluorescent or radioactive type.

Such methods comprise, for example, the following steps:

-   deposition of defined quantities of a polypeptide composition    according to the invention into the wells of a microtitre plate,-   introduction, into the said wells, of increasing dilutions of serum,    or of a different biological sample as defined above, which has to    be analysed,-   incubation of the microplate,-   introduction, into the wells of the microtitre plate, of labelled    antibodies directed against human or animal immunoglobulins, these    antibodies having been labelled with the aid of an enzyme selected    from those which are capable of hydrolyzing a substrate, thereby    modifying the absorption of the radiation of the latter, at least at    a defined wavelength, for example at 550 nm,-   detection, by comparison with a control, of the quantity of    substrate hydrolyzed.

The invention also relates to a kit or set for the detection and/or theidentification of bacteria belonging to the species Chlamydia pneumoniaeor to an associated microorganism, characterized in that it comprisesthe following components:

-   a polypeptide according to the invention,-   where appropriate, the reagents for constituting the medium    appropriate for the immunological or specific reaction,-   the reagents allowing the detection of the antigen-antibody    complexes produced by the immunological reaction between the    polypeptide(s) of the invention and the antibodies which may be    present in the biological sample, it being possible for these    reagents also to carry a label, or to be capable of being recognized    in turn by a labelled reagent, more particularly in the case where    the polypeptide according to the invention is not labelled,-   where appropriate, a reference biological sample (negative control)    free of antibodies recognized by a polypeptide according to the    invention,-   where appropriate, a reference biological sample (positive control)    containing a predetermined quantity of antibodies recognized by a    polypeptide according to the invention.

According to the invention, the polypeptides, peptides, fusion proteinsor other derivatives, or analogs thereof encoded by a polynucleotidesequence in SEQ ID No. 1, may be used as an immunogen to generateantibodies which immunospecifically bind such an immunogen. Suchantibodies may include, but are not limited to, polyclonal andmonoclonal antibodies, humanized or chimeric antibodies, single chainantibodies, Fab fragments, F(ab′)₂ fragments, fragments produced by aFab expression library, anti-idiotypic (anti-Id) antibodies, andepitope-binding fragments of any of the above. In a specific embodiment,the antibody to a polypeptide, peptide or other derivative, or analogthereof encoded by a polynucleotide sequence in SEQ ID No. 1 is abispecific antibody (see generally, e.g. Fanger and Drakeman, 1995, DrugNews and Perspectives 8: 133–137). Such a bispecific antibody isgenetically engineered to recognize both (1) an epitope and (2) one of avariety of “trigger” molecules, e.g. Fc receptors on myeloid cells, andCD3 and CD2 on T cells, that have been identified as being able to causea cytotoxic T-cell to destroy a particular target. Such bispecificantibodies can be prepared either by chemical conjugation, hybridoma, orrecombinant molecular biology techniques known to the skilled artisan.

Various procedures known in the art may be used for the production ofpolyclonal antibodies to a polypeptide, peptide or other derivative, oranalog thereof encoded by a polynucleotide sequence in SEQ ID No. 1. Forthe production of antibody, various host animals can be immunized byinjection with a polypeptide, or peptide or other derivative, or analogthereof, including but not limited to rabbits, mice, rats, etc. Variousadjuvants, depending on the host species, may be used to increase theimmunological response, including but not limited to STIMULON QS-21(Aquila Biopharmaceuticals, Inc., Framingham, Mass.), MPL(3-O-deacylated monophosphoryl lipid A; RIBI ImmunoChem Research, Inc.,Hamilton, Mont.), aluminum phosphate, IL-12 (Genetics Institute,Cambridge, Mass.), Freund's (complete and incomplete), mineral gels suchas aluminum hydroxide, surface active substances such as lysolecithin,pluronic polyols, polyanions, peptides, oil emulsions, keyhole limpethemocyanins, dinitrophenol, BCG (bacille Calmette-Guerin), andcorynebacterium parvum. Alternatively, polyclonal antibodies may beprepared by purifying, on an affinity column onto which a polypeptideaccording to the invention has been previously attached, the antibodiescontained in the serum of patients infected with a bacterium belongingto the species Chlamydia pneumoniae.

For preparation of monoclonal antibodies directed toward a polypeptide,peptide or other derivative, or analog, any technique which provides forthe production of antibody molecules by continuous cell lines in culturemay be used. For example, the hybridoma technique originally developedby Kohler and Milstein (1975, Nature 256:495–497), as well as the triomatechnique, the human B-cell hybridoma technique (Kozbor et al., 1983,Immunology Today 4:72), and the EBV-hybridoma technique to produce humanmonoclonal antibodies (Cole et al., 1985, in Monoclonal Antibodies andCancer Therapy, Alan R. Liss, Inc., pp. 77–96). In an additionalembodiment of the invention, monoclonal antibodies can be produced ingerm-free animals utilizing technology described in PCT/US90/02545. Inanother embodiment of the invention, transgenic non-human animals can beused for the production of human antibodies utilizing technologydescribed in WO 98/24893 and WO 96/33735. According to the invention,human antibodies may be used and can be obtained by using humanhybridomas (Cote et al., 1983, Proc. Natl. Acad. Sci. U.S.A.80:2026–2030) or by transforming human B cells with EBV virus in vitro(Cole et al., 1985, in Monoclonal Antibodies and Cancer Therapy, Alan R.Liss, pp. 77–96). In fact, according to the invention, techniquesdeveloped for the production of “chimeric antibodies” (Morrison et al.,1984, PROC. NATL. ACAD. SCI. U.S.A. 81:6851–6855; Neuberger et al.,1984, Nature 312:604–608; Takeda et al., 1985, Nature 314:452–454) bysplicing the genes from a mouse antibody molecule specific for apolypeptide, peptide or other derivative, or analog together with genesfrom a human antibody molecule of appropriate biological activity can beused; such antibodies are within the scope of this invention.

According to the invention, techniques described for the production ofsingle chain antibodies (U.S. Pat. No. 4,946,778) can be adapted toproduce polypeptide or peptide-specific single chain antibodies. Anadditional embodiment of the invention utilizes the techniques describedfor the construction of Fab expression libraries (Huse et al., 1989,Science 246:1275–1281) to allow rapid and easy identification ofmonoclonal Fab fragments with the desired specificity for polypeptides,derivatives, or analogs.

Antibody fragments which contain the idiotype of the molecule can begenerated by known techniques. For example, such fragments include butare not limited to: the F(ab′)₂ fragment which can be produced by pepsindigestion of the antibody molecule; the Fab′ fragments which can begenerated by reducing the disulfide bridges of the F(ab′)₂ fragment, theFab fragments which can be generated by treating the antibody moleculewith papain and a reducing agent, and Fv fragments.

In addition, techniques have been developed for the production ofchimerized (See, e.g., Boss, M. et al., U.S. Pat. No. 4,816,397; andCabilly, S. et al., U.S. Pat. No. 5,585,089 each of which isincorporated herein by reference in its entirety) humanized antibodies(See, e.g., Queen, U.S. Pat. No. 5,585,089, which is incorporated hereinby reference in its entirety.) An immunoglobulin light or heavy chainvariable region consists of a “framework” region interrupted by threehypervariable regions, referred to as complementarily determiningregions (CDRs). The extent of the framework region and CDRs have beenprecisely defined (See, “Sequences of Proteins of ImmunologicalInterest”, Kabat, E. et al., U.S. Department of Health and HumanServices (1983). Briefly, humanized antibodies are antibody moleculesfrom non-human species having one or more CDRs from the non-humanspecies and a framework from a human immunoglobulin molecule.

The antibodies of the invention may also be labelled in the same manneras described above for the nucleic probes of the invention such as anenzymatic, fluorescent or radioactive type labelling.

The invention relates, in addition, to a method for the detection and/orthe identification of bacteria belonging to the species Chlamydiapneumoniae or to an associated microorganism in a biological sample,characterized in that it comprises the following steps:

-   a) bringing the biological sample (biological tissue or fluid) into    contact with a mono- or polyclonal antibody according to the    invention (under conditions allowing an immunological reaction    between the said antibodies and the polypeptides of the bacterium    belonging to the species Chlamydia pneumoniae or to an associated    microorganism which may be present in the biological sample, that    is, under conditions suitable for the formation of immune    complexes);-   b) detecting the antigen-antibody complex which may be formed.

Also falling within the scope of the invention is a kit or set for thedetection and/or the identification of bacteria belonging to the speciesChlamydia pneumoniae or to an associated microorganism, characterized inthat it comprises the following components:

-   a polyclonal or monoclonal antibody according to the invention,    labeled where appropriate;-   where appropriate, a reagent for constituting the medium appropriate    for carrying out the immunological reaction;-   a reagent allowing the detection of the antigen-antibody complexes    produced by the immunological reaction, it being possible for this    reagent also to carry a label, or to be capable of being recognized    in turn by a labelled reagent, more particularly in the case where    the said monoclonal or polyclonal antibody is not labelled;-   where appropriate, reagents for carrying out the lysis of the cells    in the sample tested.

The principle of the DNA chip which was explained above may also be usedto produce protein “chips” on which the support has been coated with apolypeptide or an antibody according to the invention, or arraysthereof, in place of the DNA. These protein “chips” make it possible,for example, to analyze the biomolecular interactions (BIA) induced bythe affinity capture of target analytes onto a support coated, forexample, with proteins, by surface plasma resonance (SPR). Reference maybe made, for example, to the techniques for coupling proteins onto asolid support which are described in EP 524 800 or to the methodsdescribing the use of biosensor-type protein chips such as theBIAcore-type technique (Pharmacia) (Arlinghaus et al., 1997, Krone etal., 1997, Chatelier et al., 1995). These polypeptides or antibodiesaccording to the invention, capable of specifically binding antibodiesor polypeptides derived from the sample to be analysed, may thus be usedin protein chips for the detection and/or the identification of proteinsin samples. The said protein chips may in particular be used forinfectious diagnosis and may preferably contain, per chip, severalpolypeptides and/or antibodies of the invention of differentspecificity, and/or polypeptides and/or antibodies capable ofrecognizing microorganisms different from Chlamydia pneumoniae.

Accordingly, the subject of the present invention is also thepolypeptides and the antibodies according to the invention,characterized in that they are immobilized on a support, in particularof a protein chip.

The protein chips, characterized in that they contain at least onepolypeptide or one antibody according to the invention immobilized onthe support of the said chip, also form part of the invention.

The invention comprises, in addition, a protein chip according to theinvention, characterized in that it contains, in addition, at least onepolypeptide of a microorganism different from Chlamydia pneumoniae or atleast one antibody directed against a compound of a microorganismdifferent from Chlamydia pneumoniae, immobilized on the support of thesaid chip.

The invention also relates to a kit or set for the detection and/or theidentification of bacteria belonging to the species Chlamydia pneumoniaeor to an associated microorganism, or for the detection and/or theidentification of a microorganism characterized in that it comprises aprotein chip according to the invention.

The subject of the present invention is also a method for the detectionand/or the identification of bacteria belonging to the species Chlamydiapneumoniae or to an associated microorganism in a biological sample,characterized in that it uses a nucleotide sequence according to theinvention.

More particularly, the invention relates to a method for the detectionand/or the identification of bacteria belonging to the species Chlamydiapneumoniae or to an associated microorganism in a biological sample,characterized in that it comprises the following steps:

-   a) where appropriate, isolation of the DNA from the biological    sample to be analysed, or optionally production of a cDNA from the    RNA in the biological sample;-   b) specific amplification of the DNA of bacteria belonging to the    species Chlamydia pneumoniae or to an associated microorganism with    the aid of at least one primer according to the invention;-   c) detection of the amplification products.

These may be detected, for example, by the molecular hybridizationtechnique using a nucleic probe according to the invention. This probewill be advantageously labelled with a nonradioactive (cold probe) orradioactive element.

For the purposes of the present invention, “DNA in the biologicalsample” or “DNA contained in the biological sample” will be understoodto mean either the DNA present in the biological sample considered, oroptionally the cDNA obtained after the action of a reversetranscriptase-type enzyme on the RNA present in the said biologicalsample.

Another aim of the present invention consists in a method according tothe invention, characterized in that it comprises the following steps:

-   a) bringing a nucleotide probe according to the invention into    contact with a biological sample, the DNA contained in the    biological sample having, where appropriate, been previously made    accessible to hybridization, under conditions allowing the    hybridization of the probe to complementary base pairs of the DNA of    a bacterium belonging to the species Chlamydia pneumoniae or to an    associated microorganism;-   b) detecting the hybridization complex formed between the nucleotide    probe and the DNA in the biological sample.

The present invention also relates to a method according to theinvention, characterized in that it comprises the following steps:

-   a) bringing a nucleotide probe immobilized on a support according to    the invention into contact with a biological sample, the DNA in the    sample having, where appropriate, been previously made accessible to    hybridization, under conditions allowing the hybridization of the    probe to the DNA of a bacterium belonging to the species Chlamydia    pneumoniae or to an associated microorganism;-   b) bringing the hybrid formed between the nucleotide probe    immobilized on a support and the DNA contained in the biological    sample, where appropriate after removal of the DNA in the biological    sample which has not hybridized with the probe, into contact with a    labelled nucleotide probe according to the invention;-   c) detecting the new hybrid formed in step b).

According to an advantageous embodiment of the method for the detectionand/or the identification defined above, it is characterized in that,prior to step a), the DNA in the biological sample is primer-extendedand/or amplified beforehand with the aid of at least one primeraccording to the invention.

The invention relates, in addition, to a kit or set for the detectionand/or the identification of bacteria belonging to the species Chlamydiapneumoniae or to an associated microorganism, characterized in that itcomprises the following components:

-   a) a nucleotide probe according to the invention;-   b) where appropriate, the reagents necessary for carrying out a    hybridization reaction;-   c) where appropriate, at least one primer according to the invention    as well as the reagents (e.g., polymerase and/or deoxynucleotide    triphosphates) necessary for a DNA amplification reaction.

The invention also relates to a kit or set for the detection and/or theidentification of bacteria belonging to the species Chlamydia pneumoniaeor to an associated microorganism, characterized in that it comprisesthe following components:

-   a) a nucleotide probe, called capture probe, according to the    invention;-   b) an oligonucleotide probe, called detection probe, according to    the invention;-   c) where appropriate, at least one primer according to the invention    as well as the reagents (e.g., polymerase and/or deoxynucleotide    triphosphates) necessary for a DNA amplification reaction.

The invention also relates to a kit or set for the detection and/or theidentification of bacteria belonging to the species Chlamydia pneumoniaeor to an associated microorganism, characterized in that it comprisesthe following components:

-   a) at least one primer according to the invention;-   b) where appropriate, the reagents necessary for carrying out a DNA    amplification reaction;-   c) where appropriate, a component which makes it possible to check    the sequence of the amplified fragment, more particularly an    oligonucleotide probe according to the invention.

The invention relates, in addition, to a kit or set for the detectionand/or the identification of bacteria belonging to the species Chlamydiapneumoniae or to an associated microorganism, or for the detectionand/or the identification of a microorganism characterized in that itcomprises a DNA chip according to the invention.

The invention also relates to a method or to a kit or set according tothe invention for the detection and/or the identification of bacteriabelonging to the species Chlamydia pneumoniae, characterized in that thesaid primer and/or the said probe according to the invention are chosenfrom the nucleotide sequences specific to the species Chlamydiapneumoniae, in that the said polypeptides according to the invention arechosen from the polypeptides specific to the species Chlamydiapneumoniae and in that the said antibodies according to the inventionare chosen from the antibodies directed against the polypeptidesaccording to the invention chosen from the polypeptides specific to thespecies Chlamydia pneumoniae.

Preferably, the said method or the said kit or set above according tothe invention, for the detection and/or the identification of bacteriabelonging to the species Chlamydia pneumoniae is characterized in thatthe said primer and/or the said probe or the said polypeptides arechosen from the nucleotide sequences or polypeptides according to theinvention which have been identified as being specific to the speciesChlamydia pneumoniae and in that the said antibodies according to theinvention are chosen from the antibodies directed against thepolypeptides according to the invention chosen from the polypeptidesidentified as being specific to the species Chlamydia pneumoniae.

The invention relates, in addition, to a method or a kit or setaccording to the invention for the diagnosis of predispositions to, orof a condition caused by, cardiovascular diseases, preferably linked tothe presence of atheroma, which are induced or worsened by a Chlamydiapneumoniae infection.

The invention also relates to a method or a kit or set according to theinvention for the diagnosis of predispositions to, or of conditionscaused by, respiratory diseases induced or worsened by a Chlamydiapneumoniae infection; preferably, the said respiratory disease isasthma.

According to another aspect, the subject of the invention is the use ofpolypeptides according to the invention, of cells transformed with avector according to the invention and/or of transformed animalsaccording to the invention, for the biosynthesis or the biodegradationof organic or inorganic compounds.

As has been mentioned above, the nucleotide sequences of the inventionwere identified by homology with sequences known to encode, for example,polypeptides or fragments of enzymatic polypeptides involved in thebiosynthesis or the biodegradation of organic or inorganic molecules.

It is thus possible to use the said polypeptides of the invention in asimilar manner for the biosynthesis or the biodegradation of organic orinorganic compounds of industrial or therapeutic interest (calledcompounds of interest).

Among these polypeptides, there may be mentioned in particular theenzymes involved in metabolism, such as the proteolytic enzymes, aminotransferases, glucose metabolism, or the enzymes which may be used inthe biosynthesis of sugars, amino acids, fatty acids, polypeptides,nucleotides, nucleic acids or any other organic or inorganic compound orin the biodegradation of organic or inorganic compounds.

Among these polypeptides, there may be mentioned, in addition, themutated or modified enzymes corresponding to mutated or modifiedpolypeptides according to the invention which may also be used for thebiosynthesis or the biodegradation of organic or inorganic compounds atthe industrial level, such as, for example, the production of compoundsof interest, the reprocessing of manufacturing residues applied to thefood industries, to the papermaking industry or to the chemical andpharmaceutical industries.

The methods of biosynthesis or biodegradation of organic or inorganiccompounds, characterized in that they use a polypeptide or one of itsrepresentative fragments according to the invention, transformed cellsaccording to the invention and/or a transformed animal according to theinvention, also form part of the invention.

The invention relates, in addition, to the use of a nucleotide sequenceaccording to the invention, of a polypeptide according to the invention,of an antibody according to the invention, of a cell according to theinvention, and/or of a transformed animal according to the invention,for the selection of an organic or inorganic compound capable ofmodulating, regulating, inducing or inhibiting the expression of genes,and/or of modifying the cellular replication of eukaryotic orprokaryotic cells or capable of inducing, inhibiting or worsening thepathologies linked to an infection by Chlamydia pneumoniae or one of itsassociated microorganisms.

The invention also comprises screening assays that comprise methods ofselecting compounds capable of binding to a polypeptide, fusionpolypeptide or one of its representative fragments according to theinvention, capable of binding to a nucleotide sequence according to theinvention, or capable of recognizing an antibody according to theinvention, and/or capable of modulating, regulating, inducing orinhibiting the expression of genes, and/or of modifying the growth orthe cellular replication of eukaryotic or prokaryotic cells, or capableof inducing, inhibiting or worsening, in an animal or human organism,the pathologies linked to an infection by Chlamydia pneumoniae or one ofits associated microorganisms, characterized in that it comprises thefollowing steps:

a) bringing the said compound into contact with the said polypeptide,the said nucleotide sequence, with a transformed cell according to theinvention and/or administering the said compound to a transformed animalaccording to the invention;

b) determining the capacity of the said compound to bind with the saidpolypeptide or the said nucleotide sequence, or to modulate, regulate,induce or inhibit the expression of genes, or to modulate growth orcellular replication, or to induce, inhibit or worsen in the saidtransformed animal, the pathologies linked to an infection by Chlamydiapneumoniae or one of its associated microorganisms.

The transformed cells and/or animals according to the invention mayadvantageously serve as a model and may be used in methods for studying,identifying and/or selecting compounds capable of being responsible forpathologies induced or worsened by Chlamydia pneumoniae, or capable ofpreventing and/or of treating these pathologies such as, for example,cardiovascular or respiratory diseases. In particular, the transformedhost cells, in particular bacteria of the Chlamydia family whosetransformation with a vector according to the invention may, forexample, increase or inhibit its infectivity, or modulate thepathologies usually induced or worsened by the infection, may be used toinfect animals in which the onset of pathologies will be monitored.These nontransformed animals, infected for example with transformedChlamydia bacteria, may serve as a study model. In the same manner, thetransformed animals according to the invention may, for example, exhibitpredispositions to cardiovascular and/or respiratory diseases and thusbe used in methods for selecting compounds capable of preventing and/orof treating the said diseases. The said methods using the saidtransformed cells and/or transformed animals form part of the invention.

The compounds capable of being selected may be organic compounds such aspolypeptides or carbohydrates or any other organic or inorganiccompounds already known, or new organic compounds produced usingmolecular modeling techniques and obtained by chemical or biochemicalsynthesis, these techniques being known to persons skilled in the art.

The said selected compounds may be used to modulate the growth and/orthe cellular replication of Chlamydia pneumoniae or any other associatedmicroorganism and thus to control infection by these microorganisms. Thesaid compounds according to the invention may also be used to modulatethe growth and/or the cellular replication of all eukaryotic orprokaryotic cells, in particular tumour cells and infectiousmicroorganisms, for which the said compounds will prove active, themethods which make it possible to determine the said modulations beingwell known to persons skilled in the art.

Compound capable of modulating the growth of a microorganism isunderstood to designate any compound which makes it possible to act, tomodify, to limit and/or to reduce the development, the growth, the rateof proliferation and/or the viability of the said microorganism.

This modulation may be achieved, for example, by an agent capable ofbinding to a protein and thus of inhibiting or of potentiating itsbiological activity, or capable of binding to a membrane protein of theouter surface of a microorganism and of blocking the penetration of thesaid microorganism into the host cell or of promoting the action of theimmune system of the infected organism directed against the saidmicroorganism. This modulation may also be achieved by an agent capableof binding to a nucleotide sequence of a DNA or RNA of a microorganismand of blocking, for example, the expression of a polypeptide whosebiological or structural activity is necessary for the growth or for thereproduction of the said microorganism.

Associated microorganism is understood to designate in the presentinvention any microorganism whose gene expression may be modulated,regulated, induced or inhibited, or whose growth or cellular replicationmay also be modulated by a compound of the invention. Associatedmicroorganism is also understood to designate in the present inventionany microorganism containing nucleotide sequences or polypeptidesaccording to the invention. These microorganisms may, in some cases,contain polypeptides or nucleotide sequences identical or homologous tothose of the invention may also be detected and/or identified by thedetection and/or identification methods or kit according to theinvention and may also serve as a target for the compounds of theinvention.

The invention relates to the compounds capable of being selected by amethod of selection according to the invention.

The invention also relates to a pharmaceutical composition comprising acompound chosen from the following compounds:

-   a nucleotide sequence according to the invention;-   a polypeptide according to the invention;-   a vector according to the invention;-   an antibody according to the invention; and-   a compound capable of being selected by a method of selection    according to the invention, optionally in combination with a    pharmaceutically acceptable vehicle.

An effective quantity is understood to designate a sufficient quantityof the said compound or antibody, or of a polypeptide of the invention,which makes it possible to modulate the growth of Chlamydia pneumoniaeor of an associated microorganism.

The invention also relates to a pharmaceutical composition comprisingone or more polypeptides according to the invention and/or one or morefusion polypeptides according to the invention. Such compositionsfurther comprise a pharmaceutically acceptable carrier or vehicle.Pharmaceutical compositions include compositions that comprise apolypeptide or fusion polypeptide that immunoreacts with seropositiveserum of an individual infected with Chlamydia pneumoniae. In oneembodiment, a pharmaceutical composition according to the invention canbe utilized for the prevention or the treatment of an infection by abacterium belonging to the species Chlamydia pneumoniae or by anassociated microorganism.

The invention relates, in addition, to an immunogenic composition or avaccine composition, characterized in that it comprises one or morepolypeptides according to the invention and/or one or more hybrid(fusion) polypeptides according to the invention. Such compositionsfurther comprise a pharmaceutically acceptable carrier or vehicle.Immunogenic compositions or fusion polypeptide include compositions thatcomprise a polypeptide that immunoreacts with seropositive serum of anindividual infected with Chlamydia pneumoniae.

Immunogenic or vaccine compositions can also comprise DNA immunogenic orvaccine compositions comprising polynucleotide sequences of theinvention operatively associated with a regulatory sequence thatcontrols gene expression. Such compositions can include compositionsthat direct expression of a neutralizing epitope of Chlamydiapneumoniae.

The invention also comprises the use of a transformed cell according tothe invention, for the preparation of a vaccine composition.

The invention also relates to a vaccine composition, characterized inthat it contains a nucleotide sequence according to the invention, avector according to the invention and/or a transformed cell according tothe invention.

The invention also relates to the vaccine compositions according to theinvention, for the prevention or the treatment of an infection by abacterium belonging to the species Chlamydia pneumoniae or by anassociated microorganism.

The invention also relates to the use of DNA encoding polypeptides ofChlamydia pneumoniae, in particular antigenic determinants, to beformulated as vaccine compositions. In accordance with this aspect ofthe invention, the DNA of interest is engineered into an expressionvector under the control of regulatory elements, which will promoteexpression of the DNA, i.e., promoter or enhancer elements. In onepreferred embodiment, the promoter element may be cell-specific andpermit substantial transcription of the DNA only in predetermined cells.The DNA may be introduced directly into the host either as naked DNA(U.S. Pat. No. 5,679,647 incorporated herein by reference in theirentirety) or formulated in compositions with other agents which mayfacilitate uptake of the DNA including viral vectors, i.e., adenovirusvectors, or agents which facilitate immunization, such as bupivicaineand other local anesthetics (U.S. Pat. No. 5,593,972 incorporated hereinby reference in their entirety), saponins (U.S. Pat. No. 5,739,118incorporated herein by reference in their entirety) and cationicpolyamines (published international application WO 96/10038 incorporatedherein by reference in their entirety).

The DNA sequence encoding the antigenic polypeptide and regulatoryelement may be inserted into a stable cell line or cloned microorganism,using techniques, such as targeted homologous recombination, which arewell known to those of skill in the art, and described e.g., in Chappel,U.S. Pat. No. 4,215,051; Skoultchi, WO 91/06667 each of which isincorporated herein by reference in its entirety.

Such cell lines and microorganisms may be formulated for vaccinepurposes. In yet another embodiment, the DNA sequence encoding theantigenic polypeptide and regulatory element may be delivered to amammalian host and introduced into the host genome via homologousrecombination (See, Chappel, U.S. Pat. No. 4,215,051; Skoultchi, WO91/06667 each of which is incorporated herein by reference in itsentirety.

Preferably, the immunogenic and/or vaccine compositions according to theinvention intended for the prevention and/or the treatment of aninfection by Chlamydia pneumoniae or by an associated microorganism willbe chosen from the immunogenic and/or vaccine compositions comprising apolypeptide or one of its representative fragments corresponding to aprotein, or one of its representative fragments, of the cellularenvelope of Chlamydia pneumoniae. The vaccine compositions comprisingnucleotide sequences will also preferably comprise nucleotide sequencesencoding a polypeptide or one of its representative fragmentscorresponding to a protein, or one of its representative fragments, ofthe cellular envelope of Chlamydia pneumoniae.

Among these preferred immunogenic and/or vaccine compositions, the mostpreferred are those comprising a polypeptide or one of itsrepresentative fragments, or a nucleotide sequence or one of itsrepresentative fragments whose sequences are chosen from the nucleotideor amino acid sequences identified in this functional group and listedabove.

The polypeptides of the invention or their representative fragmentsentering into the immunogenic compositions according to the inventionmay be selected by techniques known to persons skilled in the art, suchas for example on the capacity of the said polypeptides to stimulate Tcells, which results, for example, in their proliferation or thesecretion of interleukins, and which leads to the production ofantibodies directed against the said polypeptides.

In mice, in which a weight dose of the vaccine composition comparable tothe dose used in humans is administered, the antibody reaction is testedby collecting serum followed by a study of the formation of a complexbetween the antibodies present in the serum and the antigen of thevaccine composition, according to the customary techniques.

According to the invention, the said vaccine compositions will bepreferably in combination with a pharmaceutically acceptable vehicleand, where appropriate, with one or more appropriate immunity adjuvants.

Various types of vaccines are currently available for protecting humansagainst infectious diseases: attenuated live microorganisms (M.bovis—BCG for tuberculosis), inactivated microorganisms (influenzavirus), acellular extracts (Bordetella pertussis for whooping cough),recombinant proteins (hepatitis B virus surface antigen),polysaccharides (pneumococci). Experiments are underway on vaccinesprepared from synthetic peptides or from genetically modifiedmicroorganisms expressing heterologous antigens. Even more recently,recombinant plasmid DNAs carrying genes encoding protective antigenswere proposed as an alternative vaccine strategy. This type ofvaccination is carried out with a particular plasmid derived from an E.coli plasmid which does not replicate in vivo and which encodes only thevaccinal protein. Animals were immunized by simply injecting the nakedplasmid DNA into the muscle. This technique leads to the expression ofthe vaccine protein in situ and to a cell-type (CTL) and a humoral type(antibody) immune response. This double induction of the immune responseis one of the main advantages of the technique of vaccination with nakedDNA.

The vaccine compositions of the present invention can be evaluated in invitro and in vivo animal models prior to host, e.g., human,administration. For example, in vitro neutralization assays such asthose described by Peterson et al. (1988) can be utilized. The assaydescribed by Peterson et al. (1988) is suitable for testing vaccinecompositions directed toward either Chlamydia pneumoniae or Chlamydiatrachomatis.

Briefly, hyper-immune antisera is diluted in PBS containing 5% guineapig serum, as a complement source. Chlamydiae (10⁴ IFU; infectiousunits) are added to the antisera dilutions. The antigen-antibodymixtures are incubated at 37EC for 45 minutes and inoculated intoduplicate confluent Hep-2 or HeLa cell monolayers contained in glassvials (e.g., 15 by 45 mm), which have been washed twice with PBS priorto inoculation. The monolayer cells are infected by centrifugation at1000×g for 1 hour followed by stationary incubation at 37E for 1 hour.Infected monolayers are incubated for 48 or 72 hours, fixed and stainedwith a Chlamydiae specific antibody, such as anti-MOMP for C.trachomatis, etc. IFUs are counted in ten fields at a magnification of200×. Neutralization titer is assigned based on the dilution that gives50% inhibition as compared to control monolayers/IFU.

The efficacy of vaccine compositions can be determined in vivo bychallenging animal models of Chlamydia pneumoniae infection, e.g., miceor rabbits, with the vaccine compositions. For example, in vivo vaccinecomposition challenge studies can be performed in the murine model ofChlamydia pneumonia infection described by Moazed et al. (1997).Briefly, male homozygous apoe deficient and/or C57 BL/6J mice areimmunized with vaccine compositions. Post-vaccination, the mice aremildly sedated by subcutaneous injection of a mixture of ketamine andxylazine, and inoculated intranasally with a total volume of 0.03–0.05ml of organisms suspended in SPG medium or with SPG alone. Theinoculations of Chlamydia pneumoniae are approximately 3×10⁷ IFU/mouse.The mice are inoculated with Chlamydia pneumoniae at 8, 10, and 12 weeksof age. Tissues are then collected from the lung, spleen, heart, etc. at1–20 weeks after the first inoculation. The presence of organisms isscored using PCR, histology and immunocytochemistry, or by quantitativeculture/IFU after tissue homogenization.

Alternatively, in vivo vaccine composition challenge studies can beperformed in the rabbit model of Chlamydia pneumoniae described byLaitinen et al. (1997). Briefly, New Zealand white rabbits (5 monthsold) are immunized with the vaccine compositions. Post-vaccination, therabbits are sedated with Hypnorm, 0.3 ml/Kg of body weight,intramuscularly, and inoculated intranasally with a total of 0.5 ml ofChlamydia pneumoniae suspended in SPG medium or with SPG alone. Theinoculations of Chlamydia pneumoniae are approximately 3×10⁷ IFU/rabbit.The rabbits are reinfected in the same manner and with the same dose 3weeks after the primary inoculation. Tissues are then collected 2 weeksafter the primary infection and 1, 2, and 4 weeks after the reinfection.The presence of Chlamydia pneumoniae is scored using PCR, histology andimmunocytochemistry, or by quantitative culture/IFU after tissuehomogenization.

The vaccine compositions comprising nucleotide sequences or vectors intowhich the said sequences are inserted are in particular described inInternational Application No. WO 90/11092 and also in InternationalApplication No. WO 95/11307.

The nucleotide sequence constituting the vaccine composition accordingto the invention may be injected into the host after having been coupledto compounds which promote the penetration of this polynucleotide insidethe cell or its transport up to the cell nucleus. The resultingconjugates may be encapsulated into polymeric microparticles, asdescribed in International Application No. WO 94/27238 (MedisorbTechnologies International).

According to another embodiment of the vaccine composition according tothe invention, the nucleotide sequence, preferably a DNA, is complexedwith the DEAE-dextran (Pagano et al., 1967) or with nuclear proteins(Kaneda et al., 1989), with lipids (Felgner et al., 1987) orencapsulated into liposomes (Fraley et al., 1980) or alternativelyintroduced in the form of a gel facilitating its transfection into thecells (Midoux et al., 1993, Pastore et al., 1994). The polynucleotide orthe vector according to the invention may also be in suspension in abuffer solution or may be combined with liposomes.

Advantageously, such a vaccine will be prepared in accordance with thetechnique described by Tacson et al. or Huygen et al. in 1996 oralternatively in accordance with the technique described by Davis et al.in International Application No. WO 95/11307.

Such a vaccine may also be prepared in the form of a compositioncontaining a vector according to the invention, placed under the controlof regulatory elements allowing its expression in humans or animals. Itis possible, for example, to use, as vector for the in vivo expressionof the polypeptide antigen of interest, the plasmid pcDNA3 or theplasmid pcDNA1/neo, both marketed by Invitrogen R & D Systems, Abingdon,United Kingdom). It is also possible to use the plasmid V1Jns.tPA,described by Shiver et al. in 1995. Such a vaccine will advantageouslycomprise, in addition to the recombinant vector, a saline solution, forexample a sodium chloride solution.

The immunogenic compositions of the invention can also be utilized aspart of methods for immunization, wherein such methods compriseadministering to a host, e.g., a human host, an immunizing amount of theimmunogenic compositions of the invention. In a preferred embodiment,the method of immunizing is a method of immunizing against Chlamydiapneumoniae.

A pharmaceutically acceptable vehicle is understood to designate acompound or a combination of compounds entering into a pharmaceutical orvaccine composition which does not cause side effects and which makes itpossible, for example, to facilitate the administration of the activecompound, to increase its life and/or its efficacy in the body, toincrease its solubility in solution or alternatively to enhance itspreservation. These pharmaceutically acceptable vehicles are well knownand will be adapted by persons skilled in the art according to thenature and the mode of administration of the active compound chosen.

As regards the vaccine formulations, these may comprise appropriateimmunity adjuvants which are known to persons skilled in the art, suchas, for example, aluminum hydroxide, a representative of the family ofmuramyl peptides such as one of the peptide derivatives ofN-acetyl-muramyl, a bacterial lysate, or alternatively incompleteFreund's adjuvant, STIMULON QS-21 (Aquila Biopharmaceuticals, Inc.,Framingham, Mass.), MPL (3-O-deacylated monophosphoryl lipid A; RIBIImmunoChem Research, Inc., Hamilton, Mont.), aluminum phosphate, IL-12(Genetics Institute, Cambridge, Mass.).

Preferably, these compounds will be administered by the systemic route,in particular by the intravenous route, by the intranasal,intramuscular, intradermal or subcutaneous route, or by the oral route.More preferably, the vaccine composition comprising polypeptidesaccording to the invention will be administered several times, spreadout over time, by the intradermal or subcutaneous route.

Their optimum modes of administration, dosages and galenic forms may bedetermined according to criteria which are generally taken into accountin establishing a treatment adapted to a patient, such as for examplethe patient's age or body weight, the seriousness of his generalcondition, tolerance of the treatment and the side effects observed.

The invention comprises the use of a composition according to theinvention for the treatment or the prevention of cardiovasculardiseases, preferably linked to the presence of atheroma, which areinduced or worsened by Chlamydia pneumoniae.

Finally, the invention comprises the use of a composition according tothe invention for the treatment or the prevention of respiratorydiseases which are induced or worsened by the presence of Chlamydiapneumoniae, preferably asthma.

Other characteristics and advantages of the invention appear in thefollowing examples and figures:

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1: Line for the production of Chlamydia pneumoniae sequences

FIG. 2: Analysis of the sequences and assembling

FIG. 3: Finishing techniques

FIG. 3 a): Assembly map

FIG. 3 b): Determination and use of the orphan ends of the contigs

EXAMPLES Experimental Procedures

Cells

The Chlamydia pneumoniae strain (CM1) used by the inventors is obtainedfrom ATCC (American Culture Type Collection) where it has the referencenumber ATCC 1360-VR.

It is cultured on HeLa 229 cells, obtained from the American TypeCulture Collection, under the reference ATCC CCL-2.1.

Culture of the Cells

The HeLa ATCC CCL-2.1 cells are cultured in 75-ml cell culture flasks(Corning). The culture medium is Dulbecco's modified cell culture medium(Gibco BRL No. 04101965) supplemented with MEM amino acids (Gibco BRLNo. 04301140) L (5 ml per 500 ml of medium) and 5% fetal calf serum(Gibco BRL No. 10270 batch 40G8260K) without antibiotics or antifungals.

The cell culture stock is maintained in the following manner. The cellcultures are examined under an inverted microscope. 24 hours afterconfluence, each cellular lawn is washed with PBS (Gibco BRL No.04114190), rinsed and then placed for 5 min in an oven in the presenceof 3 ml of trypsine (Gibco BRL No. 25200056). The cellular lawn is thendetached and then resuspended in 120 ml of culture medium, the whole isstirred in order to make the cellular suspension homogeneous. 30 ml ofthis suspension are then distributed per cell culture flask. The flasksare kept in a CO₂ oven (5%) for 48 hours at a temperature of 37° C. Thecell stock is maintained so as to have available daily 16 flasks ofsubconfluent cells. It is these subconfluent cells which will be used soas to be infected with Chlamydia. 25-ml cell culture flasks are alsoused, these flasks are prepared in a similar manner but the volumes usedfor maintaining the cells are the following: 1 ml of trypsine, 28 ml ofculture medium to resuspend the cells, 7 ml of culture medium are usedper 25-ml flask.

Infection of the Cells with Chlamydia

Initially, the Chlamydiae are obtained frozen from ATCC (−70° C.), insuspension in a volume of 1 ml. This preparation is slowly thawed, 500μl are collected and brought into contact with subconfluent cells, whichare obtained as indicated above, in a 25-ml cell culture flask,containing 1 ml of medium, so as to cover the cells. The flask is thencentrifuged at 2000 rpm in a “swing” rotor for microtitre plates, thecentrifuge being maintained at a temperature of 35° C. Aftercentrifugation, the two flasks are placed in an oven at 35° C. for threehours. 6 ml of culture medium containing cycloheximide (1 μg/ml) arethen added and the flask is stored at 35° C. After 72 hours, the levelof infection is evaluated by direct immunofluorescence and by thecytopathogenic effect caused to the cells.

Direct Immunofluorescence

Starting with infected cells, which were obtained as indicated above, acellular smear is deposited with a Pasteur pipette on a microscopeslide. The cellular smear is fixed with acetone for 10 minutes; afterdraining the acetone, the smear is covered with 30 μl of murinemonoclonal antibodies directed against MOMP (major outer membraneprotein) of Chlamydia (Syva, Biomérieux) labelled with fluoresceinisothiocyanate. The whole is then incubated in a humid chamber at atemperature of 37° C. The slides are then rinsed with water, slightlydried, and then after depositing a drop of mounting medium, a coverslipis mounted before reading. The reading is carried out with the aid of afluorescence microscope equipped with the required filters (excitationat 490 nm, emission at 520 nm).

Harvesting of the Chlamydia pneumoniae

After checking the infection by direct immunofluorescence, carried outas indicated above, the culture flasks are opened under a sterilecabinet, sterile glass beads with a diameter of the order of amillimeter are placed in the flask. The flask is closed and thenvigorously stirred while being maintained horizontally, the cellularlawn at the bottom, so that the glass beads can have a mechanical actionon the cellular lawn. Most of the cells are thus detached or broken; theeffect of the stirring is observed under an optical microscope so as toensure proper release of Chlamydiae.

Large-scale Infection of the Cell Cultures

The product of the Chlamydiae harvest (culture medium and cellulardebris) is collected with a pipette, and distributed into three cellculture flasks containing subconfluent HeLa ATCC CCL-2.1 cells, obtainedas indicated above. The cells thus inoculated are placed under gentlestirring (swing) in an oven at 35° C. After one hour, the flasks arekept horizontally in an oven so that the culture medium covers the cellsfor 3 hours. 30 ml of culture medium containing actydione (1 μg/ml) arethen added to each of the flasks. The culture flasks are then stored at35° C. for 72 hours. The cells thus infected are examined under anoptical microscope after 24 hours, the cytopathogenic effect isevaluated by the appearance of cytoplasmic inclusions which are visibleunder an inverted optical microscope. After 72 hours, the vacuolescontaining the Chlamydiae occupy the cytoplasm of the cell and push thecell nucleus sideways. At this stage, numerous cells are spontaneouslydestroyed and have left free elementary bodies in the culture medium.The Chlamydiae are harvested as described above and are either frozen at−80° C. or used for another propagation.

Purification of the Chlamydiae

The product of the Chlamydia harvests is stored at −80° C. and thawed ona water bath at room temperature. After thawing, each tube is vigorouslystirred for one minute and immersed for one minute in an ultrasound tank(BRANSON 1200); the tubes are then stirred by inverting before beingcentrifuged for 5 min at 2000 rpm. The supernatant is carefully removedand kept at cold temperature (ice). The supernatant is vigorouslystirred and then filtered on nylon filters having pores of 5 microns indiameter on a support (Nalgene) allowing a delicate vacuum to beestablished under the nylon filter. For each filtration, three nylonfilters are superposed; these filters are replaced after every 40 ml offiltrate. Two hundred milliliters of filtration product are kept at coldtemperature, and then after stirring by inverting, are centrifuged at10,000 rpm for 90 min, the supernatant is removed and the pellet istaken up in 10 ml of 10 mM Tris, vigorously vortexed and thencentrifuged at 10,000 rpm for 90 min. The supernatant is removed and thepellet is taken up in a buffer (20 mM Tris pH 8.0, 50 mM KCl, 5 mMMgCl₂) to which 800 units of DNAse I (Boehringer) are added. The wholeis kept at 37° C. for one hour. One ml of 0.5 M EDTA is then added, thewhole is vortexed and frozen at −20° C.

Preparation of the DNA

The Chlamydiae purified above are thawed and subjected to a proteinase K(Boehringer) digestion in a final volume of 10 ml. The digestionconditions are the following: 0.1 mg/ml proteinase K, 0.1×SDS at 55EC,stirring every 10 min. The product of digestion is then subjected to adouble extraction with phenol-chloroform, two volumes of ethanol areadded and the DNA is directly recovered with a Pasteur pipette havingone end in the form of a hook. The DNA is dried on the edge of the tubeand then resuspended in 500 μl of 2 mM Tris pH 7.5. The DNA is stored at4° C. for at least 24 hours before being used for the cloning.

Cloning of the DNA

After precipitation, the DNA is quantified by measuring the opticaldensity at 260 nm. Thirty μg of Chlamydia DNA are distributed into 10tubes of 1.5 ml and diluted in 300 μl of water. Each of the tubes issubjected to 10 applications of ultrasound lasting for 0.5 sec in asonicator (unisonix XL2020). The contents of the 10 tubes are thengrouped and concentrated by successive extractions with butanol (SigmaB1888) in the following manner: two volumes of butanol are added to thedilute DNA mixture. After stirring, the whole is centrifuged for fiveminutes at 2500 rpm and the butanol is removed. This operation isrepeated until the volume of the aqueous phase is less than 1 ml. TheDNA is then precipitated in the presence of ethanol and of 0.5 M sodiumacetate pH 5.4, and then centrifuged for thirty minutes at 15,000 rpm atcold temperature (4° C.). The pellet is washed with 75% ethanol,centrifuged for five minutes at 15,000 rpm and dried at roomtemperature. A tenth of the preparation is analysed on a 0.8% agarosegel. Typically, the size of the DNA fragments thus prepared is between200 and 8000 base pairs.

To allow the cloning of the DNA obtained, the ends are repaired. The DNAis distributed in an amount of 10 μg/tube, in the following reactionmedium: 100 μl final volume, 1×buffer (Biolabs 201L), 0.5 μl BSA 0.05mg/ml, 0.1 mM dATP, 0.1 mM each of dGTP, dCTP or dTTP, 60,000 IU T4 DNApolymerase. The reaction is incubated for thirty minutes at 16° C. Thecontents of each of the tubes are then grouped before carrying out anextraction with phenol-chloroform and then precipitating the aqueousphase as described above. After this step, the DNA thus prepared isphosphorylated. For that, the DNA is distributed into tubes in an amountof 10 μg per tube, and then in a final volume of 50 μl, the reaction isprepared in the following manner: 1 mM ATP, 1×kinase buffer, 10 IU T4polynucleotide kinase (Biolabs 201L). The preparation is incubated forthirty minutes at 37° C. The contents of the tubes are combined and aphenol-chloroform extraction and then a precipitation are carried out inorder to precipitate the DNA. The latter is then suspended in 1 μl ofwater and then the DNA fragments are separated according to their sizeon a 0.8% agarose gel (1×TAE). The DNA is subjected to an electric fieldof 5 V/cm and then visualized on a UV table. The fragments whose sizevaries between 1200 and 2000 base pairs are selected by cutting out thegel. The gel fragment thus isolated is placed in a tube and then the DNAis purified with the Qiaex kit (20021 Qiagen), according to theprocedure provided by the manufacturer.

Preparation of the Vector

14 μg of the cloning vector pGEM-5Zf (Proméga P2241) are diluted in afinal volume of 150 μl and are subjected to digestion with therestriction enzyme EcoRV 300 IU (Biolabs 195S) according to the protocoland with the reagents provided by the manufacturer. The whole is placedat 37° C. for 150 min and then distributed in the wells of a 0.8%agarose gel subjected to an electric field of 5 V/cm. The linearizedvector is visualized on a UV table, isolated by cuffing out the gel andthen purified by the Qiaex kit (Qiagen 20021) according to themanufacturer's recommendations. The purification products are grouped ina tube, the volume is measured and then half the volume of phenol isadded and the whole is vigorously stirred for 1 min. Half the volume ofchloroform-isoamyl alcohol 24:1 is added and vigorously stirred for 1min. The whole is centrifuged at 15,000 rpm for 5 min at 4° C., theaqueous phase is recovered and transferred into a tube. The DNA isprecipitated in the presence of 0.3 M sodium acetate, pH 5.4 and 3volumes of ethanol and placed at −20° C. for 1 hour. The DNA is thencentrifuged at 15,000 rpm for 30 min at 4° C., the supernatant isremoved while preserving the pellet, washed twice with 70% ethanol.After drying at room temperature, the DNA is suspended in 25 μl ofwater.

Phosphorylation of the Vector

25 μl of the vector prepared in the preceding step are diluted in afinal volume of 500 μl of the following reaction mixture:

After repair, the DNA is subjected to a phenol-chloroform extraction anda precipitation, the pellet is then taken up in 10 μl of water, the DNAis quantified by measuring the optical density at 260 nm. The quantifiedDNA is ligated into the vector PGEm-5Zf(+) prepared by the restrictionenzyme EcoRV and dephosphorylated (see preparation of the vector). Theligation is carried out under three conditions which vary in the ratiobetween the number of vector molecules and the number of insertmolecules. Typically, an equimolar ratio, a ratio of 1:3 and a ratio of3:1 are used for the ligations which are, moreover, carried out underthe following conditions: vector PGEm-5Zf(+) 25 ng, cut DNA, ligationbuffer in a final volume of 20 μl with T4 DNA ligase (Amersham E70042X);the whole is then placed in a refrigerator overnight and then aphenol-chloroform extraction and a precipitation are carried out in aconventional manner. The pellet is taken up in 5 μl of water.

Transformation of the Bacteria

Plating of the Bacteria

Petri dishes containing LB Agar medium containing ampicillin (50 μg/ml),Xgal (280 μg/ml) [5-bromo-4-chloro-indolyl-beta-D-galactopyranoside(Sigma B-4252)], IPTG (140 μg/ml) [isopropyl-beta-D-thiogalactoside(Sigma I-6758)] are used, 50 and 100 μl of bacteria are plated for eachof the ligations. The Petri dishes are placed upside down at 37° C. for15 to 16 hours in an oven. The number of “recombinant” positive clonesis evaluated by counting the white colonies and the blue colonies whichare thought to contain the vector alone.

Evaluation of the “Recombinant” Positive Clones

Ninety-four white colonies and two blue colonies are collected with theaid of sterile cones and are deposited at the bottom of the wells ofplates designed for carrying out the amplification techniques. 30 μl ofthe following reaction mixture are added to each well: 1.7 mM MgCl₂, 0.2mM each of dATP, dCTP, dGTP and dTTP, two synthetic oligonucleotidescorresponding to sequences flanking the cloning site on either side andorienting the synthesis of the DNA in a convergent manner (0.5 μM RP andPU primers, 1 U TAQ polymerase (GibcoBRL 18038-026)).

The colonies thus prepared are subjected to a temperature of 94° C. for5 min and then to 30 thermal cycles composed of the following steps: 94°C. for 40 s, 50° C. for 30 s, 72° C. for 180 s. The reaction is thenkept for 7 min at 72° C. and then kept at 4° C.

The amplification products are deposited on an agarose gel (0.8%),stained with ethidium bromide, subjected to electrophoresis, and thenanalysed on an ultraviolet table. The presence of an amplificationfragment having a size greater than 500 base pairs indicates thepresence of an insert. The bacterial clones are then prepared so as tostudy the sequence of their insert.

Sequencing

To sequence the inserts of the clones obtained as above, these wereamplified by PCR on bacteria cultures carried out overnight using theprimers for the vectors flanking the inserts. The sequence of the endsof these inserts (on average 500 bases on each side) was determined byautomated fluorescent sequencing on an ABI 377 sequencer, equipped withthe ABI Prism DNA Sequencing Analysis software (version 2.1.2).

Analysis of the Sequences

The sequences obtained by sequencing in a high-yield line (FIG. 1) arestored in a database; this part of the production is independent of anytreatment of the sequences. The sequences are extracted from thedatabase, avoiding all the regions of inadequate quality, that is to saythe regions for which uncertainties are observed on the sequence at morethan 95%. After extraction, the sequences are introduced into aprocessing line, the diagram of which is described in FIG. 2. In a firstpath of this processing line, the sequences are assembled by the Gap4software from R. Staden (Bonfield et al., 1995) (OS UNIX/SUN Solaris);the results obtained by this software are kept in the form of two fileswhich will be used for a subsequent processing. The first of these filesprovides information on the sequence of each of the contigs obtained.The second file represents all the clones participating in thecomposition of all the contigs as well as their positions on therespective contigs.

The second processing path uses a sequence assembler (TIGR-Asmgassembler UNIX/SUN Solaris); the results of this second processing pathare kept in the form of a file in the TIGR-Asmg format which providesinformation on the relationship existing between the sequences selectedfor the assembly. This assembler is sometimes incapable of linkingcontigs whose ends overlap over several hundreds of base pairs.

The results obtained from these two assemblers are compared with the aidof the BLAST program, each of the contigs derived from one assembly pathbeing compared with the contigs derived from the other path.

For the two processing paths, the strict assembly parameters are fixed(95% homology, 30 superposition nucleotides). These parameters avoid 3to 5% of the clones derived from eukaryotic cells being confused withsequences obtained from the clones derived from Chlamydia pneumoniae.The eukaryotic sequences are however preserved during the course of thisproject; the strategy introduced, which is described below, will bedesigned, inter alia, not to be impeded by these sequences derived fromcontaminating clones.

The results of these two assemblers are processed in a softwaredeveloped for this project. This software operates on a Windows NTplatform and receives, as data, the results derived from the STADENsoftware and/or the results derived from the TIGR-Asmg assembler, thesoftware, results, after processing of the data, in the determination ofan assembly map which gives the proximity relationship and theorientation of the contigs in relation to one another (FIG. 3 a). Usingthis assembly map, the software determines all the primers necessary forfinishing the project. This treatment, which will be detailed below, hasthe advantage of distinguishing the isolated sequences derived from thecontaminations, by the DNA eukaryotic cells, of the small-sizedsequences clearly integrated into the project by the relationships whichthey establish with contigs. In order to allow, without any risk oferror, the arrangement and the orientation of the contigs in relation toone another, a statistical evaluation of the accuracy of the names(naming) “naming” of sequence is made from the results of “contigation”.This evaluation makes it possible to give each of the clone plates, aswell as each of the subsets of plates, a weight which is inverselyproportional to probable error rate existing in the “naming” of thesequences obtained from this plate or from a subset of this plate. Inspite of a low error rate, errors may occur throughout the steps ofproduction of the clones and of the sequences. These steps are numerous,repetitive and although most of them are automated, others, like thedeposition in the sequencers, are manual; it is then possible for theoperator to make mistakes such as the inversion of two sequences. Thistype of error has a repercussion on the subsequent processing of thedata, by resulting in relationships (between the contigs) which do notexist in reality, then in attempts at directed sequencing between thecontigs which will end in failure. It is because of this that theevaluation of the naming errors is of particular importance since itallows the establishment of a probabilistic assembly map from which itbecomes possible to determine all the clones which will serve astemplate to obtain sequences separating two adjacent contigs. Table 2 ofparent U.S. application Ser. No. 60/107,078 filed Nov. 4, 1998 andFrench application 97-14673 filed Nov. 21, 1997, each of which isincorporated by reference herein in its entirety, gives the clones andthe sequences of the primers initially used during the initialoperations.

To avoid the step which consists in ordering and then preparing theclones by conventional microbiological means, outer and inner primersoriented towards the regions not yet sequenced are defined by thesoftware. The primers thus determined make it possible to prepare, byPCR, a template covering the nonsequenced region. It is the so-calledouter primers (the ones most distant from the region to be sequenced)which are used to prepare this template. The template is then purifiedand a sequence is obtained on each of the two strands during 2sequencing reactions which each use one of the 2 inner primers. In orderto facilitate the use of this approach, the two outer primers and thetwo inner primers are prepared and then stored on the same position of 4different 96-well plates. The two plates containing the outer primersare used to perform the PCRs which will serve to prepare the templates.These templates will be purified on purification columns preserving thetopography of the plates. Each of the sequences will be obtained usingprimers situated on one and then on the other of the plates containingthe inner primers. This distribution allows a very extensive automationof the process and results in a method which is simple to use forfinishing the regions not yet sequenced. Table 3 of parent U.S.application Ser. No. 60/107,078 filed Nov. 4, 1998 and Frenchapplication 97-14673 filed Nov. 21, 1997, each of which is incorporatedby reference herein in its entirety, gives the names and the sequencesof the primers used for finishing Chlamydia pneumoniae.

Finally, a number of contigs exist in a configuration where one of theirends is not linked to any other contig end (FIG. 3 b) by a connectingclone relationship (a connecting clone is defined as a clone having onesequence end on a contig and the other end of its sequence on anothercontig; furthermore, this clone must be derived from a plate or a subsetof plates with adequate naming quality). For the Chlamydia pneumoniaeproject, this particular case occurred 24 times. Two adjacent PCRprimers orienting the synthesis of the DNA towards the end of theconsensus sequence are defined for each of the orphan ends of theconsensus sequence. The primer which is closest to the end of thesequence is called the inner primer whereas the primer which is moredistant from the end of the sequence is called the outer primer. Theouter primers are used to explore the mutual relationship between theorphan ends of the different contigs. The presence of a single PCRproduct and the possibility of amplifying this product unambiguouslyusing the inner primers evokes the probable relationship between thecontigs on which the primers which allowed the amplification aresituated. This relationship will be confirmed by sequencing and willallow the connection between the orphan ends of the consensus sequences.This strategy has made it possible to obtain a complete map of theChlamydia pneumoniae chromosome and then to finish the project.

Quality Control

All the bases not determined with certainty in the chromosomal sequencewere noted and the density of uncertainties was measured on the entirechromosome. The regions with a high density of uncertainties were notedand the PCR primers spanning these regions were drawn and arerepresented in Table 4 of parent U.S. application Ser. No. 60/107,078filed Nov. 4, 1998 and French application 97-14673 filed Nov. 21, 1997each of which is incorporated by reference herein in its entirety.

The sequence of each of the PCR products was obtained with twooperational primers different from the amplification primers. Thesequences were obtained in both directions for all the PCRs (100%success).

Data Banks

Local reorganizations of major public banks were used. The protein bankused consists of the nonredundant fusion of the Genpept bank (automatedtranslation of GENBANK, NCBI; Benson et al., 1996).

The entire BLAST software (public domain, Altschul et al., 1990) forsearching for homologies between a sequence and protein or nucleic databanks was used. The significance levels used depend on the length andthe complexity of the region tested as well as the size of the referencebank. They were adjusted and adapted to each analysis.

The results of the search for homologies between a sequence according tothe invention and protein or nucleic data banks are presented andsummarized in Table 1 below.

Table 1: List of coding chromosome regions and homologies between theseregions and the sequence banks.

Legend to Table 1: Open reading frames are identified with the GenMarksoftware version 2.3A (GenePro), the template used is Chlamydiapneumoniae of order 4 on a length of 196 nucleotides with a window of 12nucleotides and a minimum signal of 0.5. The reading frames ORF2 to ORF1137 are numbered in order of appearance on the chromosome, startingwith ORF2 (ORF column). The positions of the beginning and of the endare then given in column 2 (position). When the position of thebeginning is greater than the position of the end, this means that theregion is encoded by the strand complementary to the sequence which wasgiven in the sequence SEQ ID No. 1.

All the putative products were subjected to a search for homology onGENPEPT (release 102 for SEQ ID No. 2 to SEQ ID No. 1137, and release108 for SEQ ID No. 1138 to SEQ ID No. 1291 and SEQ ID No. 6844 to SEQ IDNo. 6849) with the BLASTP software (Altschul et al. 1990). With, asparameters, the default parameters with the exception of the expectedvalue E set at 10⁵ (for SEQ ID No. 2 to SEQ ID No. 1137) and P value setat e⁻¹⁰ (for SEQ ID No. 1138 to SEQ ID No. 1291 and SEQ ID No. 6844 toSEQ ID No. 6849). Subsequently, only the identities greater than 30% (1%column) were taken into account. The description of the most homologoussequence is given in the Homology column; the identifier for the lattersequence is given in the ID column and the animal species to which thissequence belongs is given in the Species column. The Homology score isevaluated by the sum of the blast scores for each region of homology andreported in the Score column.

Materials and Methods for Transmembrane Domains:

The DAS software was used as recommended by the authors (Cserzo et al.,1997).

This method uses, to predict the transmembrane domains, templatesderived from a sampling of selected proteins. All the regions for whicha “Cutoff” greater than 1.5 was found by the program were taken intoaccount.

Additional ORF Finder Programs

For this analysis, two additional ORF finder programs were used topredict potential open reading frames of a minimum length of 74 aminoacids; Glimmer (Salzberg, S. L., Delcher, A., Kasif, S., and W. White.1998. Microbial gene identification using interpolated Markov models.Nucleic Acids Res. 26:544–548.), and an in-house written program. Thein-house program used a very simple search algorithm. The analysisrequired the that the genomic DNA sequence text be in the 5′ to 3′direction, the genome is circular, and that TAA, TAG, and TGA are stopcodons. The search parameters were as follows:

-   (1) A search for an ORF that started with a GTG codon was performed.    If no GTG codons were found, then a search for an ATG codon was    performed. However, if a GTG codon was found, then a search    downstream for a ATG codon was performed. All start and stop    nucleotide positions were recorded.-   (2) A search for an ORF that started with a TTG codon was performed.    If no TTG codons were found, then a search for a ATG codon was    performed. However, if a TTG codon was found, then a search    downstream for a ATG codon was performed. All start and stop    nucleotide positions were recorded.-   (3) The analysis described in steps 1 and 2 were repeated for the    opposite strand of DNA sequence.-   (4) A search for ORFs that determined all ORF lengths using start    and stop positions in the same reading frames was performed.-   (5) All ORFs whose DNA length was less than 225 nucleotides were    eliminated from the search.

Surface Exposed Protein Search Criteria

Potential cell surface vaccine targets are outer membrane proteins suchas porins, lipoproteins, adhesions and other non-integral proteins. InChlamydia psittaci, the major immunogens is a group of putative outermembrane proteins (POMPs) and no homologs have been found in Chlamydiapneumoniae and Chlamydia trachomatis by traditional analysis(Longbottom, D., Russell, M., Dunbar, S. M., Jones, G. E., and A. J.Herring. 1998. Molecular Cloning and Characterization of the GenesCoding for the Highly Immunogenic Cluster of 90-Kilodalton EnvelopeProteins from Chlamydia psittaci Subtype That Causes Abortion in Sheep.Infect Immun 66:1317–1324.) Several putative outer membrane proteinshave been identified in Chlamydia pneumoniae, all of which may representvaccine candidates. The major outer membrane protein (MOMP) gene (omp1)has been found in various isolates of Chlamydia pneumoniae (Jantos, CA., Heck, S., Roggendorf, R., Sen-Gupta, M., and Hegemann, J H. 1997.Antigenic and molecular analyses of different Chlamydia pneumoniaestrains. J. Clin Microbiology 35(3):620–623.) Various criteria, aslisted below, were used to identify putative surface exposed ORFs fromthe genomic DNA sequence of Chlamydia pneumoniae (French application97-14673 filed Nov. 21, 1997). Any ORF which met any one or more of theindividual criteria were listed in this category.

Protein homology searches were done using the Blastp 2.0 tool (Altschul,S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W.,and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation ofprotein database search programs. Nucleic Acids Res. 25:3389–3402.) AnORF product was labeled surface exposed if there was homology to aknown, or hypothetical, or putative surface exposed protein with a Pscore better than e⁻¹⁰.

Most, if not all, proteins that are localized to the membrane ofbacteria, via a secretory pathway, contain a signal peptide. A softwareprogram, SignalP, analyzes the amino acid sequence of an ORF for such asignal peptide (Nielsen, H., Engelbrecht. J., Brunak, S., and G. vonHeijne. 1997. Identification of prokaryotic and eukaryotic signalpeptides and prediction of their cleavage sites. Protein Engineering10:1–6.) The first 60 N-terminal amino acids of each ORF were analyzedby SignalP using the Gram-Negative software database. The outputgenerates four separate values, maximum C, maximum Y, maximum S, andmean S. The S-score, or signal region, is the probability of theposition belonging to the signal peptide. The C-score, or cleavage site,is the probability of the position being the first in the matureprotein. The Y-score is the geometric average of the C-score and asmoothed derivative of the S-score. A conclusion of either a Yes or Nois given next to each score. If all four conclusions are Yes and theC-terminal amino acid is either a phenylalanine (F) or a tyrosine (Y),the ORF product was labelled outer membrane (Struyve, M., Moons, M., andJ. Tommassen. 1991. Carboxy-terminal Phenylalanine is Essential for theCorrect Assembly of a Bacterial Outer Membrane Protein. J. Mol. Biol.218:141–148.)

The program called Psort, determines the localization of a protein basedon its signal sequence, recognition of transmembrane segments, andanalysis of its amino acid composition (Nakai, K., and M. Kanehisa.1991. Expert system for predicting protein localization sites ingram-negative bacteria. Proteins 11:95–110.) An ORF product isconsidered to be an outer membrane protein if the output data predictsthe protein as outer membrane with a certainty value of 0.5 or betterand whose value is at least twice as large as the next predictedlocalized certainty value.

Finally, ORF products that were not predicted to be outer membrane orsurface exposed, based on the above criteria, were further analyzed. Theblastp output data for these ORFs were searched using various generaland specific keywords, suggestive of known cell surface exposedproteins. An ORF was labeled surface exposed if the keywords matched hada Blastp hit, had a P score better than e⁻¹⁰, and that there was nobetter data indicating otherwise. The following is a list of thesearched keywords:

Adhesion Adhesin Invasin Invasion Extensin Omp Outer Surface Porin OuterMembrane Cell Surface Cell Wall Pilus Pilin Flagellar BtuB sheath CirChuA CopB ExeD FadL FecA FepA FhuA FmdC FomA FrpB GspD HemR HgbA HgpHmbR HmuR HMW HrcC Hrp InvG LamB LbpA LcrQ Lmpl MxiD MOMP PilE HpaA NolWNspA OpcP OpnP Opr OspA PhoE PldA Por PscC PulD PupA QuiX RafY ScrY SepCShuA SomA SpiA Tbpl Yop YscC mip TolThose ORFs that did not meet the minimum requirement for being an outermembrane protein based on the above search criteria but which werehomologous to identified outer membrane ORFs in Chlamydia trachomatiswere included. The Chlamydia trachomatis genome (French patentapplications FR97-15041, filed Nov. 28, 1997 and 97-16034 filed Dec. 17,1997) was analyzed using the above search criteria and a number of outermembrane ORFs were identified. These Chlamydia trachomatis ORFs werethen tested against the Chlamydia pneumoniae genome using Blastp. AnyChlamydia pneumoniae ORF with a Blastp P value better than e⁻¹⁰ againsta Chlamydia trachomatis outer membrane was included in this section, ifthere was no better data indicating otherwise. A list of ORFs in theChlamydia pneumoniae genome encoding putative surface exposed proteinsis set forth above in the specification.

Identification of Putative Lipoproteins in the Genome of Chlamydiapneumoniae

Lipoproteins are the most abundant post-translationally modifiedbacterial secretory proteins (Pugsley, A. P. 1993. The complete generalsecretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50–108).The characteristic features of lipoproteins are a thiol-linkeddiacylglyceride and an amine-linked monoacyl group on the cysteine thatbecomes the amino-terminal residue after signal peptide cleavage bySignal Peptidase II. (Pugsley, A. P. 1993. The complete generalsecretory pathway in Gram-negative bacteria. Microbiol. Rev. 57:50–108).The identification of putative lipoproteins from the genomic sequencingof Chlamydia pneumoniae was done by examining the deduced amino acidsequence of identified ORFs for the presence of a signal peptide with aSignal Peptidase II cleavage site analogous to the consensus sequencefor prolipoprotein modification and processing reactions (Hayashi, S.,and H. C. Wu. 1992. Identification and characterization oflipid-modified proteins in bacteria, p. 261–285. In N. M. Hooper and A.J. Turner (ed.) Lipid modification of proteins: A practical approach.Oxford University Press, New York; Sutcliffe, I. C. and R. R. B.Russell. 1995. Lipoproteins of Gram-positive bacteria. J. Bacteriol.177:1123–1128.).

Chlamydia pneumoniae ORFs were initially screened for the most basic oflipoprotein characteristics, a cysteine in the first 30 amino acids ofthe deduced protein. ORFs with a standard start codon (ATG, GTG, or TTG)and having one or more of the following characteristics were selectedfor direct analysis of their first 30 amino acids:

-   (a) Significant Signal P value (at least two out of the four values    are Yes)-   (b) PSORT value indicating membrane passage (IM-inner membrane,    Peri-periplasm, or OM-outer membrane)-   (c) Identification of the word lipoprotein among the ORF blastp data    set.-   (d) A Blastp value of <e⁻¹⁰ with a putative lipoprotein from    Chlamydia trachomatis-   (French applications 97-15041 filed Nov. 28, 1997 and 97-16034 filed    Dec. 17, 1997).    The first 30 amino acids of each ORF in this set were analyzed for    the characteristics commonly found in lipoprotein signal peptides    (Pugsley, A. P. 1993. The complete general secretory pathway in    Gram-negative bacteria. Microbiol. Rev. 57:50–108; Hayashi, S.,    and H. C. Wu. 1992. Identification and characterization of    lipid-modified proteins in bacteria, p. 261–285. In N. M. Hooper    and A. J. Turner (ed.) Lipid modification of proteins: A practical    approach. Oxford University Press, New York; Sutcliffe, I. C.    and R. R. B. Russell. 1995. Lipoproteins of Gram-positive    bacteria. J. Bacteriol. 177:1123–1128.) Putative lipoprotein signal    peptides were required to have a cysteine between amino acid 10 and    30 and reach a minimum score of three based on the following    criteria for lipoprotein signal peptides:    (a) Identification of specific amino acids in specific positions    around the cysteine which are part of the consensus Signal Peptidase    II cleavage site (Hayashi, S., and H. C. Wu. 1992. Identification    and characterization of lipid-modified proteins in bacteria, p.    261–285. In N. M. Hooper and A. J. Turner (ed.) Lipid modification    of proteins: A practical approach. Oxford University Press, New    York); Sutcliffe, I. C. and R. R. B. Russell. 1995. Lipoproteins of    Gram-positive bacteria. J. Bacteriol. 177:1123–1128). Since the    identification of the cleavage site is the most important factor in    identifying putative lipoproteins, each correctly positioned amino    acid contributed toward reaching the minimum score of three. (b) A    hydrophobic region rich in alanine and leucine prior to the cleavage    site (Pugsley, A. P. 1993. The complete general secretory pathway in    Gram-negative bacteria. Microbiol. Rev. 57:50–108) contributed    toward reaching the minimum score of three.

(c) A short stretch of hydrophilic amino acids greater than or equal to1 usually lysine or arginine following the N-terminal methionine(Pugsley, A. P. 1993. The complete general secretory pathway inGram-negative bacteria. Microbiol. Rev. 57:50–108) contributed towardreaching the minimum score of three.

A list of ORFs in the Chlamydia pneumoniae genome encoding putativelipoproteins is set forth above in the specification.

LPS-Related ORFs of Chlamydia pneumoniae

Lipopolysaccharide (LPS) is an important major surface antigen ofChlamydia cells. Monoclonal antibodies (Mab) directed against LPS ofChlamydia pneumoniae have been identified that can neutralize theinfectivity of Chlamydia pneumoniae both in vitro and in vivo (Peterson,E. M., de la Maza, L. M., Brade, L., Brade, H. 1998. Characterization ofa Neutralizing Monoclonal Antibody Directed at the Lipopolysaccharide ofChlamydia pneumonia. Infect. Immun. Aug. 66(8):3848–3855.) ChlamydialLPS is composed of lipid A and a core oligosaccharide portion and isphenotypically of the rough type (R-LPS) (Lukacova, M., Baumann, M.,Brade, L., Mamat, U., Brade, H. 1994. Lipopolysaccharide Smooth-RoughPhase Variation in Bacteria of the Genus Chlamydia. Infect. Immun. June62(6):2270–2276.) The lipid A component is composed of fatty acids whichserve to anchor LPS in the outer membrane. The core component containssugars and sugar derivatives such as a trisaccharide of3-deoxy-D-manno-octulosonic acid (KDO) (Reeves, P. R., Hobbs, M.,Valvano, M. A., Skumik, M., Whitfield, C., Coplin, D., Kido, N., Klena,J., Maskell, D., Raetz, C. R. H., Rick, P. D. 1996. BacterialPolysaccharide Synthesis and Gene Nomenclature pp. 10071–10078, ElsevierScience Ltd.). The KDO gene product is a multifunctionalglycosyltransferase and represents a shared epitope among the Chlamydia.For a review of LPS biosynthesis see, e.g., Schnaitman, C. A., Klena, J.D. 1993. Genetics of Lipopolysaccharide Biosynthesis in EntericBacteria. Microbiol. Rev. 57:655–682.

A text search of the ORF blastp results identified several genes thatare involved in Chlamydial LPS production with a P score better thane⁻¹⁰. The following key-terms were used in the text search: KDO, CPS(Capsular Polysaccharide Biosynthesis), capsule, LPS, rfa, rfb, rfc,rfe, rha, rhl, core, epimerase, isomerase, transferase,pyrophosphorylase, phosphatase, aldolase, heptose, manno, glucose, lpxB,fibronectin, fibrinogen, fucosyltransferase, lic, lgt, pgm, tolC, rol,ChoP, phosphorylcholine, waaF, PGL-Th1. A list of ORFs in the Chlamydiapneumoniae genome encoding putative polypeptides involved: inLPS-biosynthesis is set forth above in the specification.

Type III and Other Secreted Products

Type III secretion enables gram-negative bacteria to secrete and injectpathogenicity proteins into the cytosol of eukaryotic host cells (Hueck,C. J., 1998. Type III Protein Secretion Systems in Bacterial Pathogensof Animals and Plants. In Microbiology and Molecular Biology Reviews.62:379–433.) These secreted factors often resemble eukaryotic signaltransduction factors, thus enabling the bacterium to redirect host cellfunctions (Lee, C. A., 1997. Type III secretion systems: machines todeliver bacterial proteins into eukaryotic cells? Trends Microbiol.5:148–156.) In an attempt to corrupt normal cellular functions,Chlamydial pathogenicity factors injected into the host cytosol willnonetheless, as cytoplasmic constituents be processed and presented inthe context of the Major Histocompatibility Complex (MHC class I). Assuch, these pathogenicity proteins represent MHC class I antigens andwill play an important role in cellular immunity. Also included in thisset are secreted non-type III products that may play a role as vaccinecomponents.

A text search of the ORF blastp results identified genes that areinvolved in Chlamydia pneumoniae protein secretion with a P score betterthan e⁻¹⁰. The following key-terms were used in the text search in aneffort to identify surface localized or secreted products: Yop, Lcr,Ypk, Exo, Pcr, Pop, Ipa, Vir, Ssp, Spt, Esp, Tir, Hrp, Mxi, hemolysin,toxin, IgA protease, cytolysin, tox, hap, secreted and Mip.

Chlamydia pneumoniae ORFs that did not meet the above keyword searchcriteria, but have homologs in Chlamydia trachomatis that do meet thesearch criteria are included herein. The Chlamydia trachomatis genome(French patent applications FR97-15041, filed Nov. 28, 1997 and 97-16034filed Dec. 17, 1997) was analyzed using the above search criteria and anumber of ORFs were identified. These Chlamydia trachomatis ORFs weretested against the Chlamydia pneumoniae genome using Blastp. AnyChlamydia pneumoniae ORF with a Blastp P value <e⁻¹⁰ against a Chlamydiatrachomatis homolog, identified using the above search criteria, wasincluded. A list of ORFs in the Chlamydia pneumoniae genome encodingputative secreted proteins is in the specification.

Chlamydia pneumoniae: RGD Recognition Sequence

Proteins that contain Arg-Gly-Asp (RGD) attachment site, together withintegrins that serve as their receptor constitute a major recognitionsystem for cell adhesion. The RGD sequence is the cell attachment siteof a large number of adhesive extracellular matrix, blood, and cellsurface proteins and nearly half of the known integrins recognize thissequence in their adhesion protein ligands. There are many RGDcontaining microbial proteins such as the penton protein of adenovirus,the coxsackie virus, the foot and mouth virus and pertactin, a 69 kDa(kilodalton) surface protein of Bordetella pertussis, that serve asligands through which these microbes bind to integrins on the cellsurfaces and gain entry into the cell. The following provides evidencesupporting the importance of RGD in microbial adhesion:

-   a) The adenovirus penton base protein has a cell rounding activity    and when penton base was expressed in E. coli, it caused cell    rounding and cells adhered to polystyrene wells coated with the    protein. Mutant analysis showed that both these properties required    an RGD sequence. Virus mutants with amino acid substitutions in the    RGD sequence, showed much less adherence to HeLa S3 cells, and also    were delayed in virus reproduction (Bai, M., Harfe, B., and    Freimuth, P. 1993. Mutations That Alter an RGD Sequence in the    Adenovirus Type 2 Penton Base Protein Abolish Its Cell-Rounding    Activity and Delay Virus Reproduction in Flat Cells. J. Virol.    67:5198–5205).-   b) It has been shown that attachment and entry of coxsackie virus A9    to GMK cells were dependent on an RGD motif in the capsid protein    VP1. VP1 has also been shown to bind α_(v)β₃ integrin, which is a    vitronectin receptor (Roivainen, M., Piirainen, L., Hovi, T.,    Virtanen, I., Riikonen, T., Heino, J., and Hyypia, T. 1994. Entry of    Coxsackievirus A9 into Host Cells: Specific Interactions with    α_(v)β₃ Integrin, the Vitronectin Receptor Virology, 203:357–65).-   c) During the course of whooping cough, Bordetella pertussis    interacts with alveolar macrophages and other leukocytes on the    respiratory epithelium. Whole bacteria adheres by means of two    proteins, filamentous hemagglutinin (FHA) and pertussis toxin. FHA    interacts with two classes of molecules on macrophages, galactose    containing glycoconjugates and the integrin CR3. The interaction    between CR3 and-FHA involves recognition of RGD sequence at the    positions 1097–1099 in FHA (Relman, D., Tuomanen, E., Falkow, S.,    Golenbock, D. T., Saukkonen, K., and Wright, S. D. “Recognitition of    a Bacterial Adhesin by an Integrin: Macrophage CR3 Binds Filamentous    Hemagglutinin of Bordetella Pertussis.” Cell, 61:1375–1382 (1990)).-   d) Pertactin, a 69 kDa outer membrane protein of Bordetella    pertussis, has been shown to promote attachment of Chinese hamster    ovary cells (CHO). This attachment is mediated by recognition of RGD    sequence in pertactin by integrins on CHO cells and can be inhibited    by synthetic RGD containing peptide homologous to the one present in    pertactin (Leininger, E., Roberts, M., Kenimer, J. G., Charles, I.    G., Fairweather, N., Novotny, P., and Brennan, M. J. 1991.    Pertactin, an Arg-Gly-Asp containing Bordetella pertussis surface    protein that promotes adherence of mammalian cells Proc. Natl. Acad.    Sci. USA, 88:345–349).-   e) The RGD sequence is highly conserved in the VP1 protein of foot    and mouth disease virus (FMDV). Attachment of FMDV to baby hamster    kidney cells (BHK) has been shown to be mediated by VP1 protein via    the RGD sequence. Antibodies against the RGD sequence of VP1 blocked    attachment of virus to BHK cells (Fox, G., Parry, N. R., Barnett, P.    V., McGinn, B., Rowland, D. J., and Brown, F. 1989. The Cell    Attachment Site on Foot-and-Mouth Disease Virus Includes the Amino    Acid Sequence RGD (Arginine-Glycine-Aspartic Acid) J. Gen. Virol.,    70:625–637).

It has been demonstrated that bacterial adherence can be based oninteraction of a bacterial adhesin RGD sequence with an integrin andthat bacterial adhesins can have multiple binding site characteristic ofeukaryotic extracellular matrix proteins. RGD recognition is one of theimportant mechanisms used by microbes to gain entry into eukaryoticcells.

The complete deduced protein sequence of the Chlamydia pneumoniae genomewas searched for the presence of RGD sequence. There were a total of 54ORFs that had one or more RGD sequences. Not all RGD containing proteinsmediate cell attachment. It has been shown that RGD containing peptidesthat have proline immediately following the RGD sequence are inactive incell attachment assays (Pierschbacher & Ruoslahti. 1987. Influence ofstereochemistry of the sequence Arg-Gly-Asp-Xaa on binding specificityin cell adhesion. J. Biol. Chem. 262:17294–98). ORFs that had RGD, withproline as the amino acid following the RGD sequence were excluded fromthe list. Also, RGD sequence may not be available at the surface of theprotein or may be present in a context that is not compatible withintegrin binding. Since not all RGD-containing proteins are involved incell attachment, several other criteria were used to refine the list ofRGD-containing proteins. A list of ORFs in the Chlamydia pneumoniaegenome encoding polypeptides with RGD recognition sequence(s) is in thespecification.

Non-Chlamydia trachomatis ORFs

Chlamydia pneumoniae ORFs were compared to the ORFs in the Chlamydiatrachomatis genome (French patent applications FR97-15041, filed Nov.28, 1997 and 97-16034 filed Dec. 17, 1997) using Blastp. Any Chlamydiapneumoniae ORF with a Blastp P value worse than e⁻¹⁰ (i.e. >e⁻¹⁰)against Chlamydia trachomatis ORFs are included in this section. A listof ORFs in the Chlamydia pneumoniae genome which are not found inChlamydia trachomatis is set forth above in the specification.

Cell Wall Anchor Surface ORFs

Many surface proteins are anchored to the cell wall of Gram-positivebacteria via the conserved LPXTG motif (Schneewind, O., Fowler, A., andFaull, K. F. 1995. Structure of the Cell Wall Anchor of Surface Proteinsin Staphylococcus aureus. Science 268:103–106). A search of theChlamydia pneumoniae ORFs was done using the motif LPXTG. A list of ORFsin the Chlamydia pneumoniae genome encoding polypeptides anchored to thecell wall is in the specification.

ATCC Deposits

Samples of Chlamydia pneumoniae were deposited with the American TypeCulture Collection (ATCC), Rockville, Md., on Nov. 19, 1998 and assignedthe accession number VR-2634. Cells can be grown, harvested andpurified, and DNA can be prepared as discussed above. In order to enablerecovery of specific fragments of the chromosome, one can run targetedPCR reactions, whose amplification products can then be sequenced and/orcloned into any suitable vector, according to standard procedures knownto those skilled in the art.

In addition, a sample of three pools of clones covering chromosomalregions of interest were deposited with the American Type CultureCollection (ATCC), Rockville, Md., on Nov. 19, 1998 and assigned theindicated accession number:207000; 207001; and 207002. Each pool ofclones contains a series of clones. When taken together, the three poolsin the sample cover a portion of the chromosome, with a redundancy ofslightly more than two. The total number of clones in the sample is 196.

The clones cover the following three regions of interest:

-   (i) position 30,000 to 40,000 of SEQ ID No. 1, referred to as region    A;-   (ii) position 501,500 to 557,000 of SEQ ID No. 1, referred to as    region B; and-   (iii) position 815,000 to 830,000 of SEQ ID No. 1, referred to as    region C.

Table 4 lists groups of oligonucleotides to be used to amplify each ofORFs 2–1291 according to standard procedures known to those skilled inthe art. Such oligonucleotides are listed as SEQ ID Nos. 1292 to 6451.For each ORF, the following is listed: one forward primer positioned2,000 bp upstream of the beginning of the ORF; one forward primerpositioned 200 bp upstream of the beginning of the ORF; one reverseprimer positioned 2,000 bp downstream at the end of ORF, which is 2,000bp upstream of the end site of the ORF on the complementary strand; andone reverse primer 200 bp downstream at the end of ORF, which is 200 bpupstream of the end site of the ORF on the complementary strand. Thecorresponding SEQ ID Nos. for the primers are listed in Table 4, whereFp is the proximal forward primer; Fd is the distal forward primer; Bpis the proximal reverse primer; and Bd is the distal reverse primer. Thepositions of the 5′ ends of each of these primers on the nucleotidesequence of SEQ ID No. 1 are shown in Table 5.

Table 6 lists oligonucleotides (SEQ ID Nos. 6452–6843) to be used toamplify the inserts of each of the 196 clones present in the pooledsample according to standard procedures well known to those of skill inthe art. These primers can also be utilized to amplify the chromosomalregion corresponding to the region A, B or C within which the particularinsert lies. Their positions are indicated in Table 7.

The present invention is not to be limited in scope by the specificembodiments described herein, which are intended as single illustrationsof individual aspects of the invention, and functionally equivalentmethods and components are within the scope of the invention. Indeed,various modifications of the invention, in addition to those shown anddescribed herein will become apparent to those skilled in the art fromthe foregoing description and accompanying drawings. Such modificationsare intended to fall within the scope of the appended claims.

All publications and patent applications mentioned in this specificationare herein incorporated by reference to the same extent as if eachindividual publication or patent application was specifically andindividually indicated to be incorporated by reference.

Incorporation of Related Applications

This application hereby incorporates each of the provisionalapplications, non-provisional applications, and applications to whichforeign priority is claimed, as listed on the Application Data Sheetthat is associated with the subject application, by reference and intheir entireties, including any figures, tables, nucleic acid sequences,amino acid sequences, and/or drawings.

TABLE 1 ORF Begin End Homology ID Species Score I % ORF2 42 794triosephosphate isomerase L27492 Thermotoga maritima 567 54 ORF3 12581614 putative ORF4 1807 2418 polypeptide deformylase D90906Synechocystis sp. 316 40 ORF5 3393 2491 hypothetical protein Z75208Bacillus subtilis 338 42 ORF6 3639 4067 unknown U87792 Bacillus subtilis117 38 ORF7 5649 4270 putative ORF8 7463 6012 putative ORF9 8051 8962putative ORF10 9129 9959 putative ORF11 10687 10361 putative ORF12 1092711232 putative ORF13 11246 12727 amidase U49269 Moraxella catarrhalis1108 42 ORF14 12691 14190 PET112 D90913 Synechocystis sp. 1044 46 ORF1514484 17249 POMP91A U65942 Chlamydia psittaci 1074 43 ORF16 16039 15770putative ORF17 17845 20853 putative ORF18 21137 22042 putative ORF1922046 23476 putative ORF20 23681 26110 putative ORF21 26109 25861putative ORF22 26241 26978 putative ORF23 26960 27754 putative ORF2427747 28577 putative ORF25 28887 29492 POMP91A U65942 Chlamydia psittaci180 39 ORF26 29432 30028 POMP91A U65942 Chlamydia psittaci 361 51 ORF2730024 31472 POMP91A U65942 Chlamydia psittaci 879 54 ORF28 31758 32288putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 144 43ORF29 32201 33991 putative 98 kDa outer membrane protein U72499Chlamydia psittaci 1126 48 ORF30 33852 34541 putative 98 kDa outermembrane protein U72499 Chlamydia psittaci 589 62 ORF31 34783 36063POMP91B precursor U65943 Chlamydia psittaci 469 46 ORF32 36009 37529putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 1338 51ORF33 37881 39362 putative 98 kDa outer membrane protein U72499Chlamydia psittaci 671 40 ORF34 39418 39161 putative ORF35 39366 40715POMP90A precursor U65942 Chlamydia psittaci 904 47 ORF36 43076 41094putative ORF37 43800 43066 putative ORF38 44828 43785 putative ORF3945340 44753 homologous to unidentified E. coli protein M96343 Bacillussubtilis 136 44 ORF40 45752 45372 o530; This 530 aa orf is 33 pctidentical (14 gaps) to AE000184 Escherichia coli 269 43 525 residues ofan approx. 640 aa protein YHES_HAEIN SW: P44808 ORF41 46996 45701 ABCtransporter, ATP-binding protein AE000596 Helicobacter pylori 878 39(yheS) ORF42 47961 47569 putative ORF43 48960 48040 hypothetical proteinD64001 Synechocystis sp. 404 37 ORF44 51452 50133 Lon protease-likeprotein X74215 Homo sapiens 1232 54 ORF45 52606 51335 unknown Z54285Schizosaccharomyces pombe 781 47 ORF46 53684 53319 putative ORF47 5419553746 putative ORF48 55278 56453 heat-shock protein U15010 Legionellapneumophila 975 45 ORF49 56493 57266 branched chain alpha-keto acidM97391 Bacillus subtilis 329 36 dehydrogenase E1-alpha ORF50 57297 58526branched chain alpha-keto acid M97391 Bacillus subtilis 707 50dehydrogenase E1-beta ORF51 59851 58565 putative ORF52 61495 59924 ComED90903 Synechocystis sp. 134 55 ORF53 61324 62151 putative ORF54 6213262470 Hpr protein X12832 Bacillus subtilis 136 36 ORF55 62474 63733enzyme I (ptsI) U32844 Haemophilus influenzae 381 35 ORF56 63881 64186f831; This 831 aa orf is 46 pct identical (11 AE000326 Escherichia coli123 34 gaps) to 709 residues of an approx. 712 aa protein PT1A_ECOLI SW:P32670 ORF57 64611 64318 ORF107 X17014 Bacillus subtilis 128 33 ORF5865485 64673 putative ORF59 65999 65301 dnaZX-like ORF put. DNApolymerase III X06803 Bacillus subtilis 596 52 ORF60 66244 67281putative ORF61 67265 67699 putative ORF62 67703 68539 putative ORF6368805 70736 putative ORF64 69172 68831 putative ORF65 70642 71142putative ORF66 71325 72029 putative ORF67 72060 73637 putative ORF6874061 76175 YqfF D84432 Bacillus subtilis 542 44 ORF69 78351 77680porphobilinogen deaminase D28503 Clostridium josui 262 42 ORF70 7935678355 sms protein D90914 Synechocystis sp. 736 52 ORF71 79983 79693ribonuclease III (rnc) AE000579 Helicobacter pylori 98 33 ORF72 8044179938 ORF3 D64116 Bacillus subtilis 268 44 ORF73 80475 80969 putativeORF74 81296 83080 hypothetical protein Y14079 Bacillus subtilis 893 38ORF75 83291 83932 manganese superoxide dismutase X77021 Caenorhabditiselegans 622 58 ORF76 84005 84769 acetyl-CoA carboxylase beta subunit(accD) AE000604 Helicobacter pylori 602 50 ORF77 84975 85244deoxyuridinetriphosphatase (dut) U32776 Haemophilus influenzae 110 41ORF78 85123 85425 deoxyuridine 5′-triphosphate AE000596 Helicobacterpylori 265 68 nucleotidohydrolase (dut) ORF79 85397 85903 ORF2 L26916Pseudomonas aeruginosa 173 34 ORF80 85909 86583 enzyme IIANtr U18997Escherichia coli 170 42 ORF81 86626 88065 putative ORF82 89257 91026putative ORF83 91291 93030 putative ORF84 93295 94086 putative ORF8595285 94707 putative ORF86 95667 96557 putative ORF87 96317 97456putative ORF88 98435 97968 putative ORF89 99460 98426 putative ORF90100144 101325 elongation factor Tu L22216 Chlamydia trachomatis 1917 95ORF91 101457 101720 putative ORF92 101704 102273 transcription factorL10348 Thermus aquaticus thermophilus 376 49 ORF93 102356 102805ribosomal protein L11 D13303 Bacillus subtilis 458 63 ORF94 102835103530 ribosomal protein L1 Z11839 Thermotoga maritima 642 51 ORF95103549 104058 ribosomal protein L10 M89911 Streptomyces antibioticus 8231 ORF96 104096 104491 rp112 (AA 1–128) X53178 Synechocystis PCC6803 32547 ORF97 104601 108386 DNA-directed RNA polymerase beta chain X64172Staphylococcus aureus 2740 52 ORF98 108401 112054 rpoC V00339Escherichia coli 2947 54 ORF99 112033 112590 acetylornithine deacetylase(EC 5.1.1.16) M22622 Leptospira biflexa 514 62 ORF100 112672 113682transaldolase L19437 Homo sapiens 755 49 ORF101 113726 114121 putativeORF102 114711 114136 putative ORF103 115267 115755 putative ORF104115911 116543 putative ORF105 116736 118055 ATPase alpha-subunit X63855Thermus aquaticus thermophilus 934 50 ORF106 117968 118522 adenosinetriphosphatase A subunit D50528 Acetabularia acetabulum 147 32 ORF107118530 119843 V-ATPase B subunit U96487 Desulfurococcus sp. SY 751 48ORF108 119816 120457 putative ORF109 120451 122430 v-type Na-ATPaseX76913 Enterococcus hirae 264 35 ORF110 122504 122950 ATP synthase,subunit K U67478 Methanococcus jannaschii 184 31 ORF111 123528 126347valyl-tRNA synthetase X05891 Escherichia coli 1679 49 ORF112 126332129166 protein kinase-like protein U19250 Streptomyces coelicolor 427 37ORF113 134690 129213 UvrA D49911 Thermus thermophilus 3107 41 ORF114134925 136382 pyruvate kinase U83196 Chlamydia trachomatis 1748 71ORF115 137870 136482 HtrB protein X61000 Escherichia coli 147 38 ORF116137899 138240 putative ORF117 138239 137928 putative ORF118 139558138257 putative ORF119 140352 139516 YbbP AB002150 Bacillus subtilis 23146 ORF120 140498 141841 cyanide insensitive terminal oxidase Y10528Pseudomonas aeruginosa 538 50 ORF121 141855 142658 cyanide insensitiveterminal oxidase Y10528 Pseudomonas aeruginosa 310 40 ORF122 144258143050 putative ORF123 145258 144494 putative ORF124 145454 146749product similar to E. coli PhoH protein Z97025 Bacillus subtilis 836 47ORF125 147318 146767 putative ORF126 148261 147677 putative ORF127149029 152157 isoleucyl-tRNA synthetase U04953 Homo sapiens 2361 52ORF128 154108 152201 leader peptidase I D90904 Synechocystis sp. 225 47ORF129 155135 154308 putative ORF130 155141 155467 YtiA AF008220Bacillus subtilis 201 43 ORF131 155703 156779 orf 361; ranslated orfsimilarity to SW: X78969 Coxiella burnetii 863 59 RF1_SALTY peptidechain release factor 1 of Salmonella typhimurium ORF132 156748 157635product similar to E. coli PRFA2 protein Z49782 Bacillus subtilis 144 37ORF133 157653 158996 Ffh U82109 Thermus aquaticus 797 45 ORF134 159363159986 tRNA (guanine-N1)-methyltransferase U32705 Haemophilus influenzae545 49 (trmD) ORF135 159880 160446 putative ORF136 160477 160839ribosomal protein L19 X72627 Synechocystis sp. 319 50 ORF137 160898161539 putative protein highly homologous to E. D32253 Magnetospirillumsp. 427 49 coli RNase HII. ORF138 161527 162153 5′guanylate kinase (gmk)U32848 Haemophilus influenzae 385 43 ORF139 162144 162443 putativeORF140 162437 164098 methionyl-tRNA synthetase AB004537Schizosaccharomyces pombe 861 54 ORF141 165451 164228exodeoxyribonuclease V (recD) U32811 Haemophilus influenzae 432 32ORF142 166349 165411 putative ORF143 166949 168442 putative ORF144169416 171029 putative ORF145 170857 171459 putative ORF146 172652173428 putative biotin-protein ligase Z97992 Schizosaccharomyces pombe292 44 ORF147 174626 173439 putative ORF148 174816 175613 putativeORF149 175598 175954 putative ORF150 175958 176935 putative ORF151177708 176938 orf 3′of chaperonin homolog hypB S40172 Chlamydia psittaci376 74 [Chlamydia psittaci, pigeon strain P-1041, Peptide Partial, 98aa] ORF152 177128 177376 putative ORF153 179472 177841 putative M69217Chlamydia pneumoniae 2678 100 ORF154 179822 179517 putative M69217Chlamydia pneumoniae 498 99 ORF155 181793 179943 Pz-peptidase D88209Bacillus licheniformis 1088 38 ORF156 182628 181876 o247; This 247 aaorf is 51 pct identical (0 AE000174 Escherichia coli 401 42 gaps) to 117residues of an approx. 160 aa protein YPH7_CHRVI SW: P45371 ORF157184420 183074 glutamate-1-semialdehyde 2,1-aminomutase X53696Escherichia coli 823 41 ORF158 184988 184467 ORF_o211 U28377 Escherichiacoli 87 54 ORF159 185483 185112 hypothetical protein D90906Synechocystis sp. 91 33 ORF160 185902 185483 ribose 5-phosphateisomerase U28377 Escherichia coli 111 41 ORF161 186174 185839 ribose5-phosphate isomerase A U32729 Haemophilus influenzae 190 46 (SP:P27252) ORF162 187720 186587 hypothetical D83026 Bacillus subtilis 53642 ORF163 188318 190933 ATP-dependent protease binding subunit M29364Escherichia coli 2010 53 ORF164 191090 191635 putative ORF165 191547192743 putative ORF166 192969 193469 putative ORF167 194044 193610putative ORF168 194196 195809 unknown Z84395 Mycobacterium tuberculosis242 52 ORF169 196088 198073 DNA ligase (EC 6.5.1.2) M24278 Escherichiacoli 1317 46 ORF170 198132 199454 putative ORF171 199351 202818 putativeORF172 204552 202999 PcpB U60175 Sphingomonas chlorophenolica 80 41ORF173 205648 204692 putative ORF174 205807 207327 leucine tRNAsynthetase AF008220 Bacillus subtilis 1595 57 ORF175 207182 207775leucyl-tRNA synthetase X06331 Escherichia coli 363 51 ORF176 207779208267 transfer RNA-Leu synthetase M88581 Bacillus subtilis 285 43ORF177 208267 209577 KDO transferase Z31593 Chlamydia pneumoniae 2262100 ORF178 211807 211271 KDO-transferase X80061 Chlamydia psittaci 10538 ORF179 212188 211844 putative ORF180 214079 212448pyrophosphate-dependent Z32850 Ricinus communis 1003 45phosphofructokinase beta subunit ORF181 214907 214083 CinI U44893Butyrivibrio fibrisolvens 111 41 ORF182 216154 215429 putative ORF183216115 216678 putative ORF184 216728 217282 putative ORF185 217267217866 putative ORF186 218593 218261 putative ORF187 219821 218994putative ORF188 221382 220309 putative ORF189 222719 221433 GMPsynthetase M10101 Escherichia coli 1151 48 ORF190 223521 222724 IMPdehydrogenase X66859 Acinetobacter calcoaceticus 778 58 ORF191 224499225008 putative ORF192 225140 225559 putative ORF193 225555 226802putative ORF194 227800 226892 putative ORF195 228335 228072 putativeORF196 229251 228643 putative ORF197 230983 229622 YqhX D84432 Bacillussubtilis 1386 56 ORF198 231483 230983 acetyl-CoA carboxylase biotincarboxyl U38804 Porphyra purpurea 199 52 carrier protein ORF199 232063231509 elongation factor P D64001 Synechocystis sp. 282 32 ORF200 232739232053 pentose-5-phosphate-3-epimerase D90911 Synechocystis sp. 463 43ORF201 233166 234356 putative ORF202 233518 233165 putative ORF203234536 235186 ORF2 L35036 Chlamydia psittaci 570 60 ORF204 235379 236689putative ORF205 236680 237618 putative ORF206 237521 238345 putativeORF207 238281 238973 putative ORF208 238871 240115 putative ORF209240191 241564 putative ORF210 242281 241604 YqiZ D84432 Bacillussubtilis 379 39 ORF211 242933 242274 f222; This 222 aa orf is 48 pctidentical (0 AE000284 Escherichia coli 382 45 gaps) to 208 residues ofan approx. 232 aa protein YCKA_BACSU SW: P42399 ORF212 243416 242976arginine repressor protein (argR) U32800 Haemophilus influenzae 229 46ORF213 243500 244531 sialoglycoprotease U15958 Pasteurella haemolytica565 53 ORF214 244480 246021 oligopeptide permease homolog AII AF000366Borrelia burgdorferi 457 34 ORF215 246330 247811 OppAIV AF000948Borrelia burgdorferi 453 35 ORF216 247831 249174 OppA gene productX56347 Bacillus subtilis 255 37 ORF217 249437 251038 dciAE X56678Bacillus subtilis 469 37 ORF218 251325 252212 OppB gene product X56347Bacillus subtilis 652 42 ORF219 253156 254007 oligopeptidepermeaseX89237 Streptococcus pyogenes 574 48 ORF220 253974 254852 ATP bindingprotein L18760 Lactococcus lactis 433 40 ORF221 255258 256094KDO-transferase X80061 Chlamydia psittaci 106 46 ORF222 256640 257455putative ORF223 257502 258239 2-OXOGLUTARAT A47930 Spinacia oleracea 63652 ORF224 257869 257501 putative ORF225 259248 260897pyrophosphate-fructose 6-phosphate 1- M55191 Solanum tuberosum 1055 44phosphotransferase beta-subunit ORF226 262753 261788 putative ORF227263059 262757 putative ORF228 264375 263182 putative ORF229 265985264747 putative ORF230 266637 266059 putative ORF231 267338 266538putative ORF232 267922 267473 putative ORF233 269647 270771 tRNA guaninetransglycosylase L33777 Zymomonas mobilis 628 44 ORF234 272777 273145ORF 4 D00624 Bacteriophage chp1 100 41 ORF235 273253 273636 putativeORF236 273705 273977 putative ORF237 276016 275717 putative ORF238276439 276020 putative ORF239 276792 277253 putative ORF240 277318277599 putative ORF241 278578 277877 putative ORF242 279258 278554 FbpCU33937 Neisseria gonorrhoeae 312 39 ORF243 280435 279533 putative ORF244281547 280849 putative ORF245 281696 282325CMP-2-keto-3-deoxyoctulosonic acid U15192 Chlamydia trachomatis 637 63synthetase ORF246 282459 284069 CTP synthetase U15192 Chlamydiatrachomatis 2000 68 ORF247 284056 284517 ORF3 U15192 Chlamydiatrachomatis 453 65 ORF248 284606 285775 glucose 6-phosphatedehydrogenase U83195 Chlamydia trachomatis 1263 77 ORF249 285592 285987glucose 6-phosphate dehydrogenase U83195 Chlamydia trachomatis 519 79ORF250 286179 286976 glucose-6-phosphate dehydrogenase D88189Actinobacillus 216 40 isozyme actinomycetemcomitans ORF251 287583 287002putative ORF252 287951 287451 putative ORF253 288499 288816 putativeORF254 289674 288505 putative ORF255 288839 289213 putative ORF256289970 290254 putative ORF257 291931 292803 gamma-D-glutamyl-L-diaminoacid X64809 Bacillus sphaericus 95 39 endopeptidase II ORF258 293258292755 ScoS9 U43429 Streptomyces coelicolor 233 45 ORF259 293718 293272ribosomal protein L13 (rpL13) U32823 Haemophilus influenzae 364 47ORF260 294630 293953 glutamine transport ATP-binding protein Q U67524Methanococcus jannaschii 387 46 ORF261 296153 294636 putative ORF262294817 295068 putative ORF263 296354 297862 conserved hypotheticalprotein AE000586 Helicobacter pylori 641 46 ORF264 298415 297879putative ORF265 298777 298253 putative ORF266 299572 298781 putativeORF267 300487 299633 putative ORF268 301586 300702 putative ORF269302440 301571 putative ORF270 302838 302437 putative ORF271 303335302745 putative ORF272 304394 303852 putative ORF273 304606 305223 f311;This 311 aa orf is 22 pct identical (13 AE000232 Escherichia coli 250 38gaps) to 186 residues of an approx. 488 aa protein YACA_BACSU SW:P37563; pyu1 of D21139 ORF274 305394 306236 survival protein surE U81296Sinorhizobium meliloti 156 42 ORF275 306501 307439 YqfU D84432 Bacillussubtilis 547 42 ORF276 308033 307458 3-octaprenyl-4-hydroxybenzoatecarboxylyase U61168 Bacillus firmus 403 42 ORF277 308924 3080374-hydroxybenzoate octaprenyltransferase U61168 Bacillus firmus 152 40ORF278 309485 310180 putative ORF279 310426 311214 putative ORF280311597 311253 putative ORF281 312772 311780 putative ORF282 313425312772 putative ORF283 313646 313377 putative ORF284 313937 314665lysophospholipase homolog AF006678 Schistosoma mansoni 141 44 ORF285315576 314755 dnaZX X17014 Bacillus subtilis 154 39 ORF286 316157 315531unknown D26185 Bacillus subtilis 284 31 ORF287 318657 316156 DNA gyraseL47978 Aeromonas salmonicida 1785 48 ORF288 321042 318676 DNA gyrasesubunit B U35453 Clostridium acetobutylicum 1838 59 ORF289 321445 321098putative ORF290 322309 321710 putative ORF291 323190 322366 outermembrane protein AE000654 Helicobacter pylori 376 43 ORF292 323843323181 hypothetical U70214 Escherichia coli 356 37 ORF293 324878 323856ATP-binding protein (abc) U32744 Haemophilus influenzae 545 44 ORF294325340 326410 f374; This 374 aa orf is 30 pct identical (9 AE000299Escherichia coli 1194 62 gaps) to 102 residues of an approx. 512 aaprotein FLIC_SALMU SW: P06177 ORF295 326433 327836 Xas A AE000246Escherichia coli 479 33 ORF296 328465 327839 putative ORF297 329360328857 putative ORF298 330907 329357 putative ORF299 332455 330956 MgtEU18744 Bacillus firmus 203 36 ORF300 334536 332395 putative ORF301336091 334877 putative ORF302 336103 337302 putative ORF303 338129338830 putative ORF304 338965 339501 putative ORF305 339508 340143putative ORF306 340247 342967 putative ORF307 343385 343810cAMP-dependent protein kinase type I U75932 Rattus norvegicus 102 37regulatory subunit ORF308 344171 343935 acyl carrier protein (acpP)AE000570 Helicobacter pylori 198 55 ORF309 345082 344330 3-ketoacyl-ACPreductase U39441 Vibrio harveyi 598 48 ORF310 346005 345082 malonyl-CoA:Acyl carrier protein U59433 Bacillus subtilis 538 45 transacylase ORF311346784 346437 beta-ketoacyl-acyl carrier protein synthase AE000540Helicobacter pylori 273 50 III (fabH) ORF312 347029 346715beta-ketoacyl-acyl carrier protein synthase M77744 Escherichia coli 26563 III ORF313 347034 347723 recombination protein D90916 Synechocystissp. 363 42 ORF314 348075 350459 putative ORF315 350598 351071 putativeORF316 351075 352175 rifampicin resistance protein L22690 Rickettsiarickettsii 495 46 ORF317 353291 352230 putative ORF318 353442 354467pyruvate dehydrogenase E1 component, D90915 Synechocystis sp. 571 44alpha subunit ORF319 354451 354933 pyruvate dehydrogenase E1 betasubunit U09137 Arabidopsis thaliana 495 59 ORF320 355000 355449 pyruvatedehydrogenase E1 component, beta U38804 Porphyra purpurea 336 47 subunitORF321 355448 356743 F23B12.5 Z77659 Caenorhabditis elegans 759 46ORF322 355953 355642 putative ORF323 359310 356827 glycogenphosphorylase B U47025 Homo sapiens 2193 57 ORF324 359120 359377putative ORF325 359525 359908 putative ORF326 361290 359947 DnaA D89066Staphylococcus aureus 375 46 ORF327 363785 361362 hypothetical U32781Haemophilus influenzae 394 44 ORF328 364496 363888 putative ORF329364832 365290 putative ORF330 365304 365669 dpj M76470 Escherichia coli160 45 ORF331 366599 365667 NADPH thioredoxin reductase AC002329Arabidopsis thaliana 975 60 ORF332 367291 369030 ribosomal protein S1(rpS1) U32801 Haemophilus influenzae 1209 41 ORF333 369134 369808 NusAU74759 Chlamydia trachomatis 995 87 ORF334 369917 370438 NusA U74759Chlamydia trachomatis 760 87 ORF335 370365 372647 U74759 Chlamydiatrachomatis 2173 61 ORF336 372557 373066 initiation factor IF2-beta(infB; gtg start X00513 Escherichia coli 333 39 codon) ORF337 373020373442 ORF6 gene product Z18631 Bacillus subtilis 192 34 ORF338 373467374195 tRNA pseudouridine 55 synthase D90917 Synechocystis sp. 358 47ORF339 374176 375099 hypothetical 34.6 kD protein in rpsT-ileS AE000113Escherichia coli 395 39 intergenic region ORF340 375676 375083hypothetical GTP-binding protein in pth 3′ AE000219 Escherichia coli 50753 region ORF341 376173 375634 hypothetical U32723 Haemophilusinfluenzae 480 59 ORF342 376564 377643 YscU U08019 Yersiniaenterocolitica 538 37 ORF343 377956 379773 lcrD gene product X67771Yersinia enterocolitica 1302 47 ORF344 379781 380425 putative ORF345380281 381000 putative ORF346 381008 381460 putative ORF347 381460383037 4-alpha-glucanotransferase L37874 Clostridium butyricum 302 38ORF348 383257 383523 ribosomal protein L28 (rpL28) U32776 Haemophilusinfluenzae 175 55 ORF349 383553 385304 hypothetical protein D90901Synechocystis sp. 565 38 ORF350 385397 386458 comE ORF1 D64002Synechocystis sp. 187 10 ORF351 387242 386514 putative ORF352 388764387013 putative ORF353 390120 390932 methylenetetrahydrofolatedehydrogenase D64000 Synechocystis sp. 588 53 ORF354 390919 391818 f351;Residues 1–121 are 100 pct identical to AE000310 Escherichia coli 186 39YOJL_ECOLI SW: P33944 (122 aa) and aa 152–351 are 100 pct identical toYOJK_ECOLI SW: P33943 ORF355 392379 391885 small protein D90914Synechocystis sp. 387 46 ORF356 392582 392986 putative ORF357 392776393684 putative ORF358 394151 394804 RecF protein D90907 Synechocystissp. 232 34 ORF359 394928 395308 putative ORF360 395259 395990 putativeORF361 397815 395953 hypothetical U32773 Haemophilus influenzae 391 36ORF362 398850 397831 H. influenzae predicted coding region U32763Haemophilus influenzae 580 39 HI0807 ORF363 400085 399099 putativeORF364 401245 400073 YtgC AF008220 Bacillus subtilis 244 30 ORF365401474 401136 putative ORF366 402199 401423 unknown U52850Erysipelothrix rhusiopathiae 534 46 ORF367 403193 402186 putative ORF368403650 404165 putative ORF369 404343 405914 adenine nucleotidetranslocase Z49227 Arabidopsis thaliana 1280 55 ORF370 405984 407327putative ORF371 407712 408806 putative ORF372 410439 409075 putativeORF373 411826 410954 putative ORF374 412482 414302 lepA gene productX91655 Bacillus subtilis 1827 59 ORF375 415402 414407 6-phosphogluconatedehydrogenase, U32737 Haemophilus influenzae 687 51 decarboxylating(gnd) ORF376 415848 415237 6-phosphogluconate dehydrogenase, 6PGD S67873Ceratitis capitata 695 64 [Ceratitis capitata = medflies, Peptide, 481aa] ORF377 417131 415866 tyrosyl-tRNA synthetase (tyrS) J01719Escherichia coli 821 45 ORF378 417258 417566 putative ORF379 418326417454 whiG-Stv gene product X68709 Streptoverticillium griseocarneum464 41 ORF380 420057 418426 FLHA gene product X63698 Bacillus subtilis455 49 ORF381 420448 420720 ferredoxin IV M59855 Rhodobacter capsulatus174 63 ORF382 420980 421552 putative ORF383 421556 422029 putativeORF384 422461 422925 putative ORF385 423562 424320 putative ORF386424250 424591 putative ORF387 424830 426047 putative ORF388 426240427397 putative ORF389 428841 430703 GcpE D90908 Synechocystis sp. 87747 ORF390 430694 431446 YfiH U50134 Escherichia coli 136 35 ORF391431597 432100 putative ORF392 432165 432779 putative ORF393 433272432832 dihydrolipoamide succinyltransferase (sucB) U32839 Haemophilusinfluenzae 475 64 ORF394 433925 433227 dihydrolipoamidesuccinyltransferase (sucB) U32839 Haemophilus influenzae 332 45 ORF395436678 433934 alpha-ketoglutarate dehydrogenase U41762 Rhodobactercapsulatus 1530 44 ORF396 437176 438357 oxygen-independentcoproporphyrinogen III AE000628 Helicobacter pylori 442 42 oxidase(hemN) ORF397 440317 438518 putative ORF398 440001 440345 putativeORF399 441233 440517 ORF_f286 U18997 Escherichia coli 168 45 ORF400440719 441012 putative ORF401 442192 441230 putative ORF402 442888442343 putative ORF403 442371 442961 putative ORF404 443578 443003[karp] gene products M86605 Chlamydia trachomatis 505 78 ORF405 444500443526 aminopeptidase D17450 Mycoplasma salivarium 273 39 ORF406 444842444528 putative ORF407 445009 444743 putative L39923 Mycobacteriumleprae 133 33 ORF408 445718 445182 putative ORF409 445807 447804 SulpU18908 Zea mays 1307 52 ORF410 448738 447803 putative ORF411 449628448618 RuvB protein U38840 Thermotoga maritima 845 53 ORF412 450298450867 deoxycytidine triphosphate deaminase (dcd) AE000554 Helicobacterpylori 573 58 ORF413 450713 451207 putative ORF414 451211 452452hemolysin D90914 Synechocystis sp. 227 39 ORF415 452448 453659 similarto [SwissProt Accession Number D90888 Escherichia coli 96 33 P37908]ORF416 454843 453725 NifS gene product L34879 Anabaena azollae 533 38ORF417 455608 454865 hypothetical protein D90908 Synechocystis sp. 37136 ORF418 456243 457007 putative ORF419 457016 457708 putative ORF420458368 457979 unknown D26185 Bacillus subtilis 152 36 ORF421 459496458372 mutY homolog U63329 Homo sapiens 466 46 ORF422 459493 460194hypothetical protein D90914 Synechocystis sp. 98 38 ORF423 461446 460355putative ORF424 462298 461450 putative ORF425 462444 463349 enoyl-ACPreductase Y13861 Nicotiana tabacum 1008 69 ORF426 464241 463342 putativeORF427 464574 465065 putative ORF428 465129 465611 putative ORF429465571 466317 putative ORF430 466317 467093 H. pylori predicted codingregion HP0152 AE000536 Helicobacter pylori 246 36 ORF431 466999 467502putative ORF432 469691 467715 unidentified transporter-ATP bindingZ82044 Bacillus subtilis 496 45 ORF433 470691 469660 acetyl-CoAcarboxylase subunit AF008220 Bacillus subtilis 781 52 ORF434 472010470709 putative ORF435 471545 471799 putative ORF436 472359 472045putative ORF437 473523 472732 orf1 X75413 Escherichia coli 313 42 ORF438474889 473441 murE gene product Z15056 Bacillus subtilis 679 37 ORF439477323 475365 penicillin-binding protein 2 X59630 Neisseria meningitidis451 42 ORF440 478496 477597 hypothetical protein D90906 Synechocystissp. 534 52 ORF441 478722 479273 putative ORF442 479277 479705 putativeORF443 480050 481450 chromosomal replication initiator protein D90909Synechocystis sp. 793 40 DnaA ORF444 481469 482053 OrfH U35673 Borreliaburgdorferi 157 37 ORF445 482600 482025 putative ORF446 482654 484204NADH: ubiquinone oxidoreductase subunit B Z37111 Vibrio alginolyticus801 49 ORF447 484211 485170 NADH: ubiquinone oxidoreductase U32702Haemophilus influenzae 258 48 (GP: Z37111_4) ORF448 485170 485838 NADH:uniquinone oxidoreductase Z37111 Vibrio alginolyticus 543 55 ORF449485813 486580 unidentified protein of Na+-translocating D49364 Vibrioalginolyticus 488 48 NADH-quinone reductase ORF450 486976 486638putative ORF451 489071 487764 putative ORF452 489341 489090 putativeORF453 489958 489152 putative ORF454 490549 489962 putative ORF455491163 490522 putative ORF456 491396 491112 putative ORF457 492121491390 putative ORF458 492304 494838 ClpC adenosine triphosphataseU02604 Bacillus subtilis 2370 46 ORF459 495943 494822 hypotheticalprotein in purB 5′ region AE000213 Escherichia coli 927 53 ORF460 496011496565 putative ORF461 496569 497228 putative ORF462 497358 497834putative ORF463 497770 498327 putative ORF464 499209 499589 putativeORF465 499520 499792 putative ORF466 500774 504169 putative 98 kDa outermembrane protein U72499 Chlamydia psittaci 1215 45 ORF467 504139 504600putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 319 47ORF468 504865 506877 putative 98 kDa outer membrane protein U72499Chlamydia psittaci 992 42 ORF469 506790 507671 putative 98 kDa outermembrane protein U72499 Chlamydia psittaci 739 46 ORF470 507718 510507putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 1813 42ORF471 508325 507912 putative ORF472 510660 513440 POMP90A precursorU65942 Chlamydia psittaci 1830 46 ORF473 514965 513787 hypotheticalD83026 Bacillus subtilis 482 48 ORF474 517347 515419 putative 98 kDaouter membrane protein U72499 Chlamydia psittaci 1554 51 ORF475 517058517363 putative ORF476 517798 517277 putative 98 kDa outer membraneprotein U72499 Chlamydia psittaci 222 41 ORF477 518200 517847 POMP91Bprecursor U65943 Chlamydia psittaci 162 42 ORF478 518300 521146 putative98 kDa outer membrane protein U72499 Chlamydia psittaci 1900 45 ORF479521392 522948 POMP91A U65942 Chlamydia psittaci 490 39 ORF480 523244524809 putative 98 kDa outer membrane protein U72499 Chlamydia psittaci507 35 ORF481 524379 524125 putative ORF482 524649 526238 putative 98kDa outer membrane protein U72499 Chlamydia psittaci 969 41 ORF483526265 527104 putative ORF484 526947 526702 putative ORF485 526975528450 putative 98 kDa outer membrane protein U72499 Chlamydia psittaci197 48 ORF486 528408 529199 putative outer membrane protein U72499Chlamydia psittaci 154 37 ORF487 530612 529542 putative ORF488 531656530616 putative ORF489 533974 532067 putative ORF490 536432 534324putative ORF491 537150 536707 putative ORF492 537928 537080 putativeORF493 538438 537932 putative ORF494 538737 538333 putative ORF495539594 539127 putative ORF496 541215 539590 putative ORF497 542571541282 putative ORF498 543014 542457 putative ORF499 543369 542962putative ORF500 543809 546628 putative 98 kDa outer membrane proteinU72499 Chlamydia psittaci 506 89 ORF501 546619 549525 POMP91A U65942Chlamydia psittaci 128 50 ORF502 547293 546994 putative ORF503 549699550523 putative 98 kDa outer membrane protein U72499 Chlamydia psittaci96 32 ORF504 550490 551551 putative 98 kDa outer membrane protein U72499Chlamydia psittaci 223 33 ORF505 551448 552623 putative 98 kDa outermembrane protein U72499 Chlamydia psittaci 139 46 ORF506 552652 555117putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 487 48ORF507 555029 555493 putative ORF508 558006 555673 putative ORF509559694 558162 putative ORF510 558208 558573 putative ORF511 561692559899 putative ORF512 561412 561708 putative ORF513 563942 5617771,4-alpha-glucan branching enzyme X73903 Streptomyces coelicolor 1743 45ORF514 564969 563950 putative ORF515 566204 564936 YqeV D84432 Bacillussubtilis 639 38 ORF516 567717 566302 putative GTPase required for highfrequency U00005 Escherichia coli 686 41 lysogenization by bacteriophagelambda ORF517 568526 567708 putative ORF518 569467 568742 putativeORF519 571065 569431 putative ORF520 571828 571118 arginine-bindingperiplasmic protein 1 AE000188 Escherichia coli 197 45 precursor ORF521572202 573308 putative ORF522 573146 575056 putative ORF523 575023575916 carboxysome formation protein D90901 Synechocystis sp. 557 59ORF524 577891 576497 putative ORF525 578914 578204 putative ORF526579924 578857 putative ORF527 580187 579858 protein kinase C inhibitorD90906 Synechocystis sp. 260 49 ORF528 580017 580406 putative ORF529581086 580187 Yer156cp U18917 Saccharomyces cerevisiae 176 34 ORF530581367 581828 putative ORF531 581678 582367 putative ORF532 582361583428 putative ORF533 584690 583431 putative ORF534 585237 584950putative ORF535 585626 586888 hypothetical protein D64004 Synechocystissp. 805 45 ORF536 586846 587907 putative ORF537 589049 588180 putativeORF538 590500 589301 putative ORF539 590755 592458 aminoacyl-tRNAsynthetase L25105 Chlamydia trachomatis 2125 71 ORF540 592526 592903 hashomology to putative heat shock L25105 Chlamydia trachomatis 324 59proteins of Bacillus subtilis and Clostridium acetobutylicum; ORFA;putative ORF541 592836 593747 Possible negative regulator of CIRCEU52216 Chlamydia trachomatis 960 65 element; Homologs in B. subtilis andClostridia spp. referred to as hrcA or orfA ORF542 593747 594298 grpEM62819 Chlamydia trachomatis 661 71 ORF543 594331 595947 DnaK proteinhomolog; 71,550 Da; putative M69227 Chlamydia pneumoniae 2619 100 ORF544595905 596309 DnaK protein homolog; 71,550 Da; putative M69227 Chlamydiapneumoniae 674 100 ORF545 596514 597215 putative ORF546 597184 597957vacB gene product U14003 Escherichia coli 306 48 ORF547 597755 598612ORF-2 D11024 Shigella flexneri 168 46 ORF548 598602 599204 homologous toDNA glycosylases; D83026 Bacillus subtilis 374 47 hypothetical ORF549599373 599939 putative ORF550 600903 602072 hemolysin X73141 Serpulinahyodysenteriae 362 36 ORF551 602240 602587 hypothetical protein D90908Synechocystis sp. 182 35 ORF552 602637 603272 putative ORF553 603142604512 putative ORF554 604627 605853 conserved hypothetical proteinAE000579 Helicobacter pylori 423 40 ORF555 605790 606620 putative ORF556606571 607281 putative L14679 Lactococcus lactis 384 45 ORF557 609004607355 putative ORF558 610906 609932 putative ORF559 611786 611004diaminopimelate epimerase D90917 Synechocystis sp. 207 55 ORF560 612333611746 ATP-dependent Clp protease proteolytic D90915 Synechocystis sp.389 44 subunit ORF561 613897 612341 serine hydroxymethyltransferaseD90903 Synechocystis sp. 909 52 ORF562 615179 616279 putative ORF563616610 617383 putative ORF564 618796 617810 ORF_o328 U18997 Escherichiacoli 413 45 ORF565 620004 618826 branched chain alpha-keto acid M97391Bacillus subtilis 688 41 dehydrogenase E2 ORF566 619649 619918 putativeORF567 621265 620021 Hypothetical protein Y14083 Bacillus subtilis 72737 ORF568 622359 621265 hypothetical U32691 Haemophilus influenzae 29452 ORF569 623420 622560 rRNA methylase D90913 Synechocystis sp. 244 38ORF570 624297 623335 hypothetical protein (SP: P39587) U67605Methanococcus jannaschii 147 35 ORF571 624773 624174 riboflavin synthasealpha chain AE000261 Escherichia coli 424 50 ORF572 625029 625484 ORF168 D28752 Synechococcus sp. 323 43 ORF573 625488 625883 YteA AF008220Bacillus subtilis 172 35 ORF574 625892 626395 signalpeptidase II X78084Staphylococcus carnosus 204 38 ORF575 626444 627790 D-alanine permease(dagA) U32770 Haemophilus influenzae 566 33 ORF576 627912 628607putative ORF577 628774 629697 putative ORF578 629660 631639 POMP91AU65942 Chlamydia psittaci 579 44 ORF579 631725 633551 putative ORF580633520 636957 putative 98 kDa outer membrane protein U72499 Chlamydiapsittaci 266 45 ORF581 637232 638098 adhesion protein D90903Synechocystis sp. 267 38 ORF582 640648 639593 GTP-binding protein D90901Synechocystis sp. 759 45 ORF583 640979 640728 50S ribosomal protein L27U38804 Porphyra purpurea 265 65 ORF584 641327 641007 50S ribosomalsubunit protein L21 U18997 Escherichia coli 210 41 ORF585 641687 642283hypothetical protein D90906 Synechocystis sp. 76 39 ORF586 643023 642286assimilatory sulfite reductase L26503 Saccharomyces cerevisiae 284 42ORF587 643330 643076 putative ORF588 643704 643351 ribosomal protein S10(rpS10) U32761 Haemophilus influenzae 349 69 ORF589 645628 643676translation elongation factor EF-G (fusA) AE000625 Helicobacter pylori1991 58 ORF590 645783 645538 elongation factor G (AA 1–691) X16278Thermus aquaticus thermophilus 170 80 ORF591 646269 645793 ribosomalprotein S7 Z11567 Chlamydia trachomatis 730 88 ORF592 646751 646314ribosomal protein S12 (AA 1–123) X52912 Cryptomonas phi 485 67 ORF593647848 647045 putative ORF594 648393 650336 ORF of prc gene (alt.)D00674 Escherichia coli 554 42 ORF595 651016 650420 hypotheticalsulfur-rich protein U41759 Chlamydia psittaci 301 50 ORF596 652956651289 60 kDa CrP X53511 Chlamydia pneumoniae 2951 100 ORF597 653395653126  9 kDa CrP X53511 Chlamydia pneumoniae 502 99 ORF598 655740654193 glutamyl-tRNA synthetase homolog U41759 Chlamydia psittaci 225982 ORF599 656508 655966 early stage-specific transcription L13598Chlamydia psittaci 666 62 experimentally demonstrated; early upstreamopen reading frame (EUO) ORF600 658140 657022 unknown U41759 Chlamydiapsittaci 950 44 ORF601 660216 658525 RecJ recombination protein U41759Chlamydia psittaci 807 73 ORF602 663238 660248 protein-export membraneprotein SecD D64000 Synechocystis sp. 413 41 ORF603 664461 663157putative ORF604 665735 664635 putative ORF605 666212 666994 hypotheticalprotein D64006 Synechocystis sp. 538 58 ORF606 666998 667921 o298; This298 aa orf is 33 pct identical (24 AE000238 Escherichia coli 253 45gaps) to 248 residues of an approx. 256 aa protein CDSA_ECOLI SW: P06466ORF607 667909 668568 cytidylate kinase AE000193 Escherichia coli 400 48ORF608 668502 669203 hypothetical protein D90915 Synechocystis sp. 22533 ORF609 669154 670893 arginyl-tRNA-synthetase D64006 Synechocystis sp.1365 49 ORF610 672226 670853 UDP-N-acetylglucosamine enolpyruvyl U32788Haemophilus influenzae 642 40 transferase (murZ) ORF611 671137 671424putative ORF612 672453 673001 putative ORF613 673072 674721 putativeORF614 674549 674262 putative ORF615 675518 674796 ORF246 gene productX59551 Escherichia coli 520 43 ORF616 676083 675499 putative ORF617676630 676067 putative ORF618 677016 676600 ORF3 D10279 Bacillussubtilis 361 63 ORF619 677647 677015 peptide release factor 2 X99401Bacillus firmus 427 43 ORF620 677990 678259 unknown Z49939 Saccharomycescerevisiae 175 48 ORF621 679444 680097 unknown D26185 Bacillus subtilis263 38 ORF622 680097 680897 unknown D64126 Bacillus subtilis 506 45ORF623 681637 680849 putative ORF624 681409 682281 putative ORF625682453 682821 putative ORF626 682763 683902 sensor protein L39904Myxococcus xanthus 190 48 ORF627 684616 683969 putative ORF628 685169684534 putative ORF629 685986 685117 putative ORF630 686278 687288NtrC/NifA-like protein regulator U17902 Escherichia coli 820 45 ORF631687483 688151 putative ORF632 688740 689501 putative ORF633 690242689622 putative ORF634 690470 691126 unknown Z48008 Saccharomycescerevisiae 380 46 ORF635 692600 691497 putative ORF636 692674 695064phenylalanyl-tRNA synthetase beta-subunit U32810 Haemophilus influenzae593 45 (pheT) ORF637 695049 696032 putative ORF638 697964 696585OppC-like protein D85103 Synechococcus sp. 371 37 ORF639 699803 698274OppB gene product X56347 Bacillus subtilis 197 40 ORF640 701926 699788AppA U20909 Bacillus subtilis 324 43 ORF641 703196 702567 putativeORF642 704221 703208 putative ORF643 704240 705289 ferrochelatase X73417Arabidopsis thaliana 266 42 ORF644 706070 705300 histidine periplasmicbinding protein P29 U58045 Campylobacter jejuni 128 31 ORF645 706841706254 conserved hypothetical protein AE000592 Helicobacter pylori 15537 ORF646 707596 706811 putative ORF647 708666 707677 ADP-glucosepyrophosphorylase X55650 Solanum tuberosum 595 43 ORF648 709793 709119pyrE-F gene product X71842 Arabidopsis thaliana 400 44 ORF649 711523710132 transcription termination factor J01673 Escherichia coli 1251 60ORF650 712236 711523 putative ORF651 714734 712125 DNA polymerase IJ04479 Streptococcus pneumoniae 1334 43 ORF652 715759 714761 protease IVU67512 Methanococcus jannaschii 101 55 ORF653 717538 715886 adeninenucleotide translocase Z49227 Arabidopsis thaliana 832 39 ORF654 719113720243 replicative DNA helicase D26185 Bacillus subtilis 776 44 ORF655720590 722422 homologous to E. coli gidA X62540 Pseudomonas putida 157552 ORF656 722406 723056 putative ORF657 723551 723120 nucleoside5′-diphosphate J05207 Myxococcus xanthus 451 62 phosphotransferase (EC2.7.4.6) ORF658 724246 723626 Holliday junction DNA helicase (ruvA)U32716 Haemophilus influenzae 293 43 ORF659 724754 724251 crossoverjunction endodeoxyribonuclease U32717 Haemophilus influenzae 296 53(ruvC) ORF660 725868 724900 putative ORF661 727115 726270 putativeORF662 728126 727119 glyceraldehyde-3-phosphate dehydrogenase U83198Chlamydia trachomatis 1340 75 ORF663 728594 728208 ribosomal protein L17L33834 Chlamydia trachomatis 439 82 ORF664 729614 728604 RNA polymerasealpha-subunit L33834 Chlamydia trachomatis 1356 89 ORF665 729778 729533RNA polymerase alpha-subunit L33834 Chlamydia trachomatis 273 82 ORF666730149 729751 ribosomal protein S11 L33834 Chlamydia trachomatis 562 90ORF667 730539 730174 ribosomal protein S13 L33834 Chlamydia trachomatis544 89 ORF668 731983 730598 homolog L25077 Chlamydia trachomatis 1956 83ORF669 732427 731996 ribosomal protein CtrL15e M80325 Chlamydiatrachomatis 563 77 ORF670 732917 732423 ribosomal protein CtrS5e M80325Chlamydia trachomatis 702 84 ORF671 733598 733320 ribosomal protein L6M60652 Chlamydia trachomatis 316 87 ORF672 733869 733492 ribosomalprotein L6 M60652 Chlamydia trachomatis 469 77 ORF673 734298 733900ribosomal protein CtrS8e M80325 Chlamydia trachomatis 572 82 ORF674734858 734319 ribosomal protein CtrL5e M80325 Chlamydia trachomatis 73090 ORF675 735195 734863 ribosomal protein CtrL24e M80325 Chlamydiatrachomatis 420 70 ORF676 735578 735342 ribosomal protein CtrL14e M80325Chlamydia trachomatis 270 95 ORF677 735861 735604 ribosomal protein S17eM80325 Chlamydia trachomatis 322 77 ORF678 736492 736079 50S ribosomalprotein L16 D90905 Synechocystis sp. 439 60 ORF679 737192 736524ribosomal protein S3 D64071 Actinobacillus 612 58 actinomycetemcomitansORF680 737555 737211 ribosomal protein L22 Z21677 Thermotoga maritima228 48 ORF681 738688 737837 50S ribosomal subunit protein L2 U18997Escherichia coli 769 62 ORF682 739048 738713 putative ORF683 739736739065 ribosomal protein L4 X67014 Bacillus stearothermophilus 308 46ORF684 740477 739773 ribosomal protein L3 Z46265 Thermus aquaticusthermophilus 463 50 ORF685 740659 740958 putative ORF686 741722 740721putative ORF687 742789 741827 methionyl-tRNA formyltransferase D64001Synechocystis sp. 511 48 ORF688 743618 742782 UDP-N-acetylglucosamineacyltransferase L22690 Rickettsia rickettsii 542 43 ORF689 744092 743634(3R)-hydroxymyristol acyl carrier protein D90910 Synechocystis sp. 33955 dehydrase ORF690 744604 744107 UDP-3-0-acyl N-acetylglcosamine D90902Synechocystis sp. 287 45 deacetylase ORF691 744953 744498UDP-3-O-acyl-GlcNAc deacetylase U67855 Pseudomonas aeruginosa 262 51ORF692 746608 744986 apolipoprotein N-acyltransferase (cute) U32716Haemophilus influenzae 194 50 ORF693 747085 746621 low homology to P14protein of D78189 Bacillus subtilis 235 37 Heamophilus influenzar and14.2 kDa protein of Escherichia coli ORF694 747974 747219 polymerase IIIM22996 Bacillus subtilis 180 34 ORF695 748594 748169 hypotheticalprotein D90914 Synechocystis sp. 160 43 ORF696 749145 748573 putativeORF697 749652 749957 trxA L39892 Chlamydia psittaci 393 72 ORF698 750446749979 spoU L39892 Chlamydia psittaci 559 72 ORF699 751219 750446 mipL39892 Chlamydia psittaci 948 60 ORF700 753042 751291 aspartyl-tRNAsynthetase D90910 Synechocystis sp. 1347 47 ORF701 754309 753020histidine - tRNA ligase Z17214 Streptococcus equisimilis 757 44 ORF702755120 756175 hexosephosphate transport protein M89480 Salmonellatyphimurium 870 49 ORF703 756120 756485 hexosephosphate transportprotein M89479 Escherichia coli 321 45 ORF704 756499 760227 DNApolymerase III alpha-subunit (dnaE) AE000646 Helicobacter pylori 1977 42ORF705 761217 760297 putative ORF706 761297 761809 putative ORF707761782 762282 putative ORF708 762260 762895 putative ORF709 762867763316 hypothetical protein D90908 Synechocystis sp. 177 43 ORF710763780 763325 putative ORF711 763861 765168 DD-carboxypeptidase M85047Bacillus subtilis 292 37 ORF712 766809 765697 fmu and fmv protein D90902Synechocystis sp. 130 36 ORF713 768051 766888 putative ORF714 768566768321 putative ORF715 769342 768551 putative ORF716 770532 769378putative ORF717 771451 770804 putative ORF718 773058 7718473-phosphoglycerate kinase U83197 Chlamydia trachomatis 1540 72 ORF719773094 773456 putative ORF720 774376 773093 putative phosphate permeaseU84890 Mesembryanthemum crystallinum 870 45 ORF721 775123 774380putative ORF722 775398 774916 putative ORF723 775046 776077 sporulationprotein M57689 Bacillus subtilis 698 43 ORF724 776070 777041 was dppEU00039 Escherichia coli 565 56 ORF725 777964 777536 orf288; translatedorf similarity to SWISS- Y10436 Coxiella burnetii 256 46 PROT:YGI2_PSEPU hypothetical 32.4 kDa protein of Pseudomomas putida ORF726778176 777904 B. subtilis genes rpmH, rnpA, 50 kd, gidA X62539 Bacillussubtilis 112 37 and gidB ORF727 778621 779334 putative ORF728 781173780307 f406; This 406 aa orf is 28 pct identical (12 AE000263Escherichia coli 603 40 gaps) to 264 residues of an approx. 440 aaprotein YAOA_SCHPO SW: Q10089 ORF729 781526 781116 f406; This 406 aa orfis 28 pct identical (12 AE000263 Escherichia coli 258 45 gaps) to 264residues of an approx. 440 aa protein YAOA_SCHPO SW: Q10089 ORF730782784 781555 f423; This 423 aa orf is 29 pct identical (1 AE000263Escherichia coli 197 44 gaps) to 172 residues of an approx. 488 aaprotein YC24_CYAPA SW: P48260 ORF731 783572 782805 hypotheticalchloroplast ORF 16 U38804 Porphyra purpurea 597 52 ORF732 785032 783581ABC transporter subunit D64004 Synechocystis sp. 1720 62 ORF733 786412785360 putative ORF734 788429 786450 pbp Y14206 Streptomyces coelicolor148 55 ORF735 788944 788528 penicillin-binding protein 3 X84053Pseudomonas aeruginosa 148 38 ORF736 789758 788901 putative ORF737790332 791504 major outer membrane protein M64064 Chlamydia pneumoniae2028 99 ORF738 791846 792721 ribosomal protein S2 U60196 Chlamydiatrachomatis 904 70 ORF739 792724 793569 elongation factor Ts U60196Chlamydia trachomatis 1023 71 ORF740 793580 794323 UMP kinase U60196Chlamydia trachomatis 891 72 ORF741 794304 794843 ribosome-releasingfactor U60196 Chlamydia trachomatis 673 73 ORF742 795217 795732 unknownD26185 Bacillus subtilis 105 42 ORF743 795722 796795 unknown D26185Bacillus subtilis 208 33 ORF744 798735 797053 putative L33796 Vibriocholerae 386 34 ORF745 799823 798681 putative ORF746 799297 799578putative ORF747 801313 799808 Pkn5 U40656 Myxococcus xanthus 345 33ORF748 802453 801332 putative ORF749 803299 802457 putative ORF750803811 803290 putative ORF751 805151 803826 YscN U02499 Yersiniaenterocolitica 1185 53 ORF752 805860 805156 putative ORF753 806604806332 putative ORF754 806913 806608 putative ORF755 808222 806903putative ORF756 808751 808146 putative ORF757 809437 808673 putativeORF758 809939 809454 putative ORF759 811235 810213 delta-aminolevulinatesynthase (EC M30785 Escherichia coli 172 40 2.3.1.37) ORF760 811779813056 DNA gyrase subunit B U35453 Clostridium acetobutylicum 584 38ORF761 812890 812516 putative ORF762 812954 813583 DNA gyrase subunit BZ19108 Spiroplasma citri 371 39 ORF763 813587 815023 gyrA X92503Mycobacterium smegmatis 414 55 ORF764 815420 815746 putative ORF765816036 817010 orf-X; hypothetical protein; Method: U48870 Bacillussubtilis 569 47 conceptual translation supplied by author ORF766 817111817356 unknown Z74024 Mycobacterium tuberculosis 114 34 ORF767 817791818609 3-deoxy-d-manno-octulosonic acid 8- Z50747 Chlamydia psittaci1112 78 phosphate synthetase ORF768 818609 819094 protein of unknownfunction Z50747 Chlamydia psittaci 545 65 ORF769 819104 819823 ATPbinding protein U72493 Chlamydia trachomatis 1099 88 ORF770 820722819826 putative ORF771 822313 821000 putative ORF772 823503 822238putative ORF773 823678 825612 putative ORF774 825461 826312 putativeORF775 827280 826645 putative ORF776 828604 827171 76 kDa protein L23921Chlamydia pneumoniae 2179 100 ORF777 830026 828713 76 kDa protein L23921Chlamydia pneumoniae 1162 100 ORF778 831047 830085 mviB homolog U50732Chlamydia trachomatis 982 58 ORF779 831725 831051 mviB homolog U50732Chlamydia trachomatis 740 65 ORF780 832220 833098 T05H10.2 Z47812Caenorhabditis elegans 407 34 ORF781 833851 833396 ribosomal protein S4(rps4) AE000633 Helicobacter pylori 372 53 ORF782 834068 835039 This ORFis homologous to a 40.0 kd L22217 Mycoplasma-like organism 377 49hypothetical protein in the htrB 3′ region from E. coli, AccessionNumber X61000 ORF783 835792 835127 uridine kinase L31783 Mus musculus436 43 ORF784 837624 836116 ORF_f397 U29581 Escherichia coli 92 38ORF785 838951 840882 putative ORF786 840869 842185 exodeoxyribonucleaseV (recB) U32811 Haemophilus influenzae 409 40 ORF787 841989 843455 DNAhelicase II U39703 Mycoplasma genitalium 110 46 ORF788 843242 844021exodeoxyribonuclease V (recB) U32811 Haemophilus influenzae 196 40ORF789 845018 843987 MreC protein M31792 Escherichia coli 76 53 ORF790846174 844990 aspartate aminotransferase (aspC) X03629 Escherichia coli754 40 ORF791 848509 846311 GreA U02878 Rickettsia prowazekii 190 35ORF792 848568 849014 putative ORF793 849082 850488 NADH: ubiquinoneoxidoreducatase subunit U32702 Haemophilus influenzae 445 37 A (GP:Z37111_2) ORF794 851512 850574 porphobilinogen synthase U38348Chlorobium vibrioforme 769 45 ORF795 852064 852447 putative ORF796852398 853690 putative ORF797 855118 854243 geranylgeranyl pyrophosphatesynthase D85029 Arabidopsis thaliana 408 41 ORF798 855751 855128 f147;This 147 aa orf is 26 pct identical (1 AE000143 Escherichia coli 187 36gaps) to 99 residues of an approx. 728 aa protein E2BE_RABIT SW: P47823ORF799 856551 855829 membrane associated regulatory protein M28368Salmonella typhimurium 172 36 ORF800 856730 858556 unknown functionZ32530 Chlamydia trachomatis 842 35 ORF801 858717 859601exodeoxyribonuclease V (recD) U32811 Haemophilus influenzae 182 51ORF802 859591 860205 exonuclease V alpha subunit (AA 1–608) X04582Escherichia coli 235 45 ORF803 861132 860284 putative ORF804 861426861163 30S ribosomal protein S20 Z67753 Odontella sinensis 153 41 ORF805861701 862921 putative ORF806 863026 864798 major sigma factor U04442Chlamydia psittaci 2661 94 ORF807 864831 865256 putative ORF808 865226866581 dihydropterin pyrophosphokinase/ Y08611 Pisum sativum 455 48dihydropteroate synthase ORF809 866562 867119 dehydrofolate reductase,type I (folA) U32772 Haemophilus influenzae 213 49 ORF810 867025 867816M. jannaschii predicted coding region U67522 Methanococcus jannaschii207 36 MJ0768 ORF811 867820 868497 putative ORF812 869743 868661 RecAU16739 Chlamydia trachomatis 1512 87 ORF813 870633 870094 unknownfunction Z32530 Chlamydia trachomatis 308 45 ORF814 871929 870646unknown function Z32530 Chlamydia trachomatis 1410 63 ORF815 872538872086 putative ORF816 873908 872517 putative ORF817 874281 874670nifR3-like gene product Z37984 Azospirillum brasilense 181 32 ORF818874582 875286 ORF1 gene product X62399 Escherichia coli 307 42 ORF819877857 875377 DNA topoisomerase I L27797 Bacillus subtilis 1488 50ORF820 878446 879255 putative ORF821 880635 879268 sigma factor (ntrA)(AA 1–502) X05888 Azotobacter vinelandii 257 47 ORF822 882524 880593 DNAhelicase II D90906 Synechocystis sp. 1140 50 ORF823 882612 883319ipa-57d gene product X73124 Bacillus subtilis 601 51 ORF824 884155883538 hypothetical protein D90915 Synechocystis sp. 344 39 ORF825884340 885611 19/20 residue stretch (32–51) identical to N- L19954Bacillus subtilis 456 37 terminal putative signal sequence of unknown,partly cloned B. subtilis gene.; putative ORF826 885722 887302 heatshock protein L12004 Chlamydia trachomatis 915 39 ORF827 887587 888153bas1 protein Z34917 Hordeum vulgare 474 50 ORF828 888627 888220 putativeORF829 889330 888716 hypothetical protein Y14079 Bacillus subtilis 22355 ORF830 889898 889323 peptidoglycan-associated lipoprotein X65796Escherichia coli 222 50 ORF831 891190 889898 TolB U32470 Haemophilusinfluenzae 280 35 ORF832 891828 891247 putative ORF833 892421 892017exbD peptide M28819 Escherichia coli 77 48 ORF834 893116 892421 innermembrane protein (tolQ) U32722 Haemophilus influenzae 157 54 ORF835892521 892925 putative ORF836 893392 895419 inner membrane coppertolerance protein Z36905 Escherichia coli 120 35 ORF837 895745 896527unknown D26185 Bacillus subtilis 381 41 ORF838 896668 897558 succinatedehydrogenase subunit C Y08563 Paenibacillus macerans 253 40 ORF839897565 899442 succinate dehydrogenase subunit A Y08563 Paenibacillusmacerans 1667 57 ORF840 899420 900229 succinate dehydrogenase subunit BY08563 Paenibacillus macerans 656 54 ORF841 903230 900237 putativeORF842 905081 903234 putative ORF843 906931 905045 sigma factor SibGregulation protein RsbU D90905 Synechocystis sp. 117 35 ORF844 907248907832 putative ORF845 907784 908128 putative ORF846 908132 908677putative ORF847 908589 909320 putative ORF848 909405 911465 putativeORF849 911677 912360 putative ORF850 912303 912821 putative ORF851912937 913983 putative ORF852 915128 914067 putative ORF853 916658915303 enolase L29475 Bacillus subtilis 1036 60 ORF854 915627 915376enolase U43738 Mycoplasma pneumoniae 226 65 ORF855 917707 916853excinuclease ABC subunit B (uvrB) U32804 Haemophilus influenzae 724 46ORF856 918837 917722 excinuclease ABC subunit B (uvrB) U32804Haemophilus influenzae 1029 54 ORF857 919868 918837 tryptophanyl-tRNAsynthetase (trpS) U32746 Haemophilus influenzae 376 40 ORF858 920434919880 putative ORF859 921187 920438 ORF8 X82078 Chlamydia sp. 164 50ORF860 921959 921195 hypothetical protein X62475 Chlamydia psittaci 51144 ORF861 923773 921995 Threonyl tRNA Synthetase Z80360 Bacillussubtilis 1476 44 ORF862 922146 922415 putative ORF863 923943 923674putative ORF864 924077 925006 putative ORF865 925436 925083 putativeORF866 926524 925349 putative ORF867 927920 926433 putative ORF868928319 927951 putative ORF869 928963 928334 putative ORF870 929248930987 DNA mismatch repair protein (mutL) U32692 Haemophilus influenzae585 40 ORF871 930995 932059 YqhT D84432 Bacillus subtilis 445 39 ORF872932121 933515 putative ORF873 932881 932513 putative ORF874 933485935746 pulD (ttg start codon) M32613 Klebsiella pneumoniae 210 33 ORF875935724 937082 epsE M96172 Vibrio cholerae 890 55 ORF876 937229 938410PilG U32588 Neisseria gonorrhoeae 280 38 ORF877 938281 938805 putativeORF878 938809 939255 putative ORF879 939165 939782 putative ORF880939760 940791 putative ORF881 940822 941106 putative ORF882 940977941351 putative ORF883 942537 941623 yscT L25667 Yersiniapseudotuberculosis 169 44 ORF884 942784 942500 yscS L25667 Yersiniapseudotuberculosis 173 42 ORF885 943149 942799 HrcR AE000107 Rhizobiumsp. NGR234 265 52 ORF886 943799 943029 pathogenicity protein M64094Xanthomonas campestris 252 41 ORF887 944055 943732 putative M74011Yersinia enterocolitica 112 33 ORF888 944413 943994 putative ORF889945395 944556 putative ORF890 945853 945389 putative ORF891 946392945751 HrcJ U56662 Erwinia amylovora 229 44 ORF892 947410 948081putative ORF893 949871 948915 ORF YOR196c Z75104 Saccharomycescerevisiae 702 44 ORF894 951058 949868 dihydrolipoamide dehydrogenase E3subunit M57435 Bacillus subtilis 745 39 ORF895 951249 950959dihydrolipoamide acetyltransferase E3 M73535 Staphylococcus aureus 16649 subunit ORF896 951664 952134 putative ORF897 952674 952165 SNF X98455Bacillus cereus 229 47 ORF898 953491 952589 helicase U39680 Mycoplasmagenitalium 307 42 ORF899 955324 953495 F01G4.1 Z68341 Caenorhabditiselegans 133 57 ORF900 955823 955281 putative ORF901 957082 955847branched-chain amino acid carrier Z48676 Lactobacillus delbrueckii 29740 ORF902 957902 957270 endonuclease III U11289 Bacillus subtilis 317 37ORF903 959231 957906 homologous to E. coli 50 K X62539 Bacillus subtilis805 45 ORF904 959376 960284 phosphatidylserine decarboxylase U72715Chlamydia trachomatis 776 51 ORF905 960266 961669 putative ORF906 961856964765 secretory component U06928 Caulobacter crescentus 1812 55 ORF907966855 965395 28.2% of identity to the Escherichia coli L47648 Bacillussubtilis 778 41 GTP-binding protein Era; putative ORF908 968204 966975poly(A) polymerase L47709 Bacillus subtilis 383 41 ORF909 968791 968237ClpX-like protein U18229 Bacillus subtilis 340 39 ORF910 969498 968731ATP-dependent protease ATPase subunit D64006 Synechocystis sp. 846 66ORF911 969858 969511 ClpP U16135 Synechococcus sp. 257 54 ORF912 970118969762 ATP-dependent clp protease proteolytic AE000591 Helicobacterpylori 362 63 component (clpP) ORF913 970593 970300 putative ORF914971261 970542 putative ORF915 971680 971123 putative ORF916 971876975100 SNF X98455 Bacillus cereus 778 49 ORF917 975419 976516 MreBprotein M96343 Bacillus subtilis 960 55 ORF918 976584 978320 phosphoenol pyruvate carboxykinase S56812 Chlorobium limicola 1667 64 ORF919977680 977231 putative ORF920 978399 980738 putative ORF921 980756981928 putative ORF922 982974 981931 precursor protein (AA − 22 to 371)X52557 Chlamydia trachomatis 97 50 ORF923 984120 983119 NAD + dependentglycerol-3-phosphate L47648 Bacillus subtilis 618 43 dehydrogenaseORF924 985502 984120 AgX-1 antigen [human, infertile patient, S73498Homo sapiens 254 34 testis, Peptide, 505 aa] ORF925 987180 985882 ORF 4M72718 Bacillus subtilis 697 38 ORF926 987172 987444 putative ORF927989846 989049 nifU-like protein AE000542 Helicobacter pylori 302 31ORF928 991048 989846 putative ORF929 991638 990955 phosphoglyceromutaseL09651 Zymomonas mobilis 471 53 ORF930 991794 992498 ORFX13 L09228Bacillus subtilis 403 39 ORF931 993619 993041 biotin[acetyl-CoA-carboxylase] ligase L47709 Bacillus subtilis 136 38 ORF932993530 994792 rod-shape-determining protein M22857 Escherichia coli 31244 ORF933 995970 994795 cadmium-transporting ATPase D64005 Synechocystissp. 358 47 ORF934 996857 995739 ATPase L28104 Transposon Tn5422 449 39ORF935 997603 996782 putative ORF936 998969 997572 seryl-trna synthetaseY09924 Staphylococcus aureus 851 42 ORF937 998896 1000023 orf2,homologue to B. subtilis ribG X64395 Escherichia coli 596 40 ORF9381000087 1001340 GTP cyclohydrolase II D90912 Synechocystis sp. 1078 52ORF939 1001357 1001818 riboflavin synthase beta subunit U27202Actinobacillus pleuropneumoniae 278 36 ORF940 1003288 1001873 putativeORF941 1003487 1004146 putative ORF942 1004485 1005639 D-alanine glycinepermease (dagA) AE000603 Helicobacter pylori 394 33 ORF943 10056431005972 hypothetical protein MTCY180.08 Z97193 Mycobacteriumtuberculosis 274 58 ORF944 1006784 1006116 similar to trithorax proteinin final three U13875 Caenorhabditis elegans 155 46 exons ORF945 10075631006769 yycJ D78193 Bacillus subtilis 406 38 ORF946 1009226 1007568 YtpTAF008220 Bacillus subtilis 992 47 ORF947 1009989 1009336 putative ORF9481015852 1016337 putative ORF949 1016561 1016181 putative ORF950 10162971017532 putative ORF951 1016802 1016452 putative ORF952 1018993 1017701phenolhydroxylase component U32702 Haemophilus influenzae 909 47 ORF9531019454 1019137 ORF M63939 Escherichia coli 96 45 ORF954 1020764 1019562pCTHom1 gene product M94254 Chlamydia trachomatis 1185 65 ORF955 10214051021037 histone H1-like protein M80324 Chlamydia psittaci 319 62 ORF9561021821 1024286 phosphoprotein L25078 Chlamydia trachomatis 739 41ORF957 1024697 1024248 putative ORF958 1025569 1024508protoporphyrinogen oxidase U25114 Mus musculus 86 38 ORF959 10269691025590 oxygen independent coprophorphyrinogen D90912 Synechocystis sp.880 42 III oxidase ORF960 1027789 1026947 uroporphyrinogen decarboxylaseM97208 Bacillus subtilis 372 38 ORF961 1031199 1027945transcription-repair coupling factor (trcF) U32805 Haemophilusinfluenzae 1584 42 (mfd) ORF962 1031717 1031172 alanyl-tRNA synthetaseX95571 Thiobacillus ferrooxidans 76 31 ORF963 1033057 1031612alanyl-tRNA synthetase AE000353 Escherichia coli 889 40 ORF964 10334251033039 alanyl-tRNA synthetase (alaS) AE000629 Helicobacter pylori 32751 ORF965 1033784 1033200 alanyl-tRNA synthetase X59956 Rhizobiumleguminosarum 416 47 ORF966 1033963 1036038 transketolase Z73234Bacillus subtilis 1398 44 ORF967 1036945 1036010 AMP nucleosidaseAE000290 Escherichia coli 265 42 ORF968 1037110 1037679 elongationfactor P U14003 Escherichia coli 458 51 ORF969 1037696 1037944 putativeORF970 1038916 1037975 putative ORF971 1040582 1039026 HSP60 chaperoninX62914 Clostridium perfringens 284 31 ORF972 1040997 1042337 PROBABLEUDP-N- AB001488 Bacillus subtilis 446 39 ACETYLMURAMOYLALANYL-D-GLUTAMYL-2, 6-DIAMINOLIGASE (EC 6.3.2.15). ORF973 1042357 1043403 ORF-Y(AA 1–360) X51584 Escherichia coli 582 45 ORF974 1043367 1044623UDP-N-acetylmuramoylalanine-D- U32793 Haemophilus influenzae 348 42glutamate ligase (murD) ORF975 1044607 1045362 hypothetical proteinY14079 Bacillus subtilis 115 38 ORF976 1045384 1046538 spoVE geneproduct (AA 1–366) X51419 Bacillus subtilis 479 35 ORF977 10464471047517 mur Y13922 Enterococcus hirae 256 45 ORF978 1047521 1049956UDP-N-acetylmuramate-alanine ligase U32794 Haemophilus influenzae 756 38(murC) ORF979 1050611 1050036 unknown Z74024 Mycobacterium tuberculosis78 44 ORF980 1050925 1050566 cycY gene product U14003 Escherichia coli179 34 ORF981 1051728 1051090 putative ORF982 1051743 1052063hypothetical protein D90908 Synechocystis sp. 135 33 ORF983 10521011053126 trna delta(2)-isopentenylpyrophosphate Z98209 Mycobacteriumtuberculosis 441 37 transferase ORF984 1054201 1053107 conservedhypothetical protein AE000579 Helicobacter pylori 826 44 ORF985 10542421055555 putative ORF986 1055483 1055908 putative ORF987 1056609 1056965YqeL D84432 Bacillus subtilis 202 38 ORF988 1056961 1058232beta-ketoacyl-ACP synthase L13242 Ricinus communis 1266 55 ORF9891058238 1058687 diadenosine tetraphosphatase U30313 Homo sapiens 122 42ORF990 1059371 1058727 inorganic pyrophosphatase (ppa) AE000576Helicobacter pylori 209 39 ORF991 1059526 1060578 leucine dehydrogenaseLeuDH U51099 Bacillus cereus 680 45 ORF992 1061553 10605793′(2′),5′-bisphosphate nucleotidase U40433 Arabidopsis thaliana 335 43ORF993 1061674 1062411 putative ORF994 1062377 10640772-acylglycerophosphoethanolamine acyl U29581 Escherichia coli 383 44transferase/acyl carrier protein synthetase ORF995 1064116 10652437-keto-8-aminopelargonic acid synthetase M29291 Bacillus sphaericus 20035 (bioF) ORF996 1067451 1065178 priA Y10304 Bacillus subtilis 1009 43ORF997 1068065 1067376 putative ORF998 1068209 1068706 putative ORF9991069958 1068819 unknown U41759 Chlamydia psittaci 777 41 ORF1000 10711631070033 unknown U41759 Chlamydia psittaci 381 36 ORF1001 1072438 1071332unknown U41759 Chlamydia psittaci 254 37 ORF1002 1072997 1073476putative ORF1003 1074239 1075864 lysyl-tRNA synthetase D90906Synechocystis sp. 1007 48 ORF1004 1076790 1075867 cysteinyl-tRNAsynthetase L14580 Bacillus subtilis 395 52 ORF1005 1077268 1076573cys-tRNA synthetase (cysS) U32693 Haemophilus influenzae 431 56 ORF10061077999 1078724 putative ORF1007 1079088 1078672 ribonuclease P proteincomponent (gtg start M11056 Escherichia coli 78 46 codon) ORF10081079642 1079944 30S ribosomal subunit protein S14 U18997 Escherichiacoli 260 50 ORF1009 1080501 1079995 F18C12.2 Z75536 Caenorhabditiselegans 118 38 ORF1010 1080775 1081341 putative ORF1011 1083158 1081350deoxyribodipyrimidine photolyase J03294 Bacillus subtilis 687 44 ORF10121084677 1083235 DNA mismatch repair protein U71154 Aquifex pyrophilus735 48 ORF1013 1085648 1084632 DNA mismatch repair protein D90909Synechocystis sp. 565 39 ORF1014 1086117 1086737 DNA primase (dnaG)U32735 Haemophilus influenzae 303 40 ORF1015 1086692 1087897 DnaG Z83860Mycobacterium tuberculosis 222 37 ORF1016 1088646 1089005 putativeORF1017 1089146 1089805 putative ORF1018 1092931 1089890 glycyl-tRNAsynthetase U20547 Chlamydia trachomatis 2569 48 ORF1019 1093179 1092889putative ORF1020 1093584 1094204 phosphatidylglycerophosphate synthaseU87792 Bacillus subtilis 163 55 ORF1021 1095619 1094192 glycogen(starch) synthase D90899 Synechocystis sp. 574 40 ORF1022 10960741096628 partial ctc gene product (AA 1–186) X16518 Bacillus subtilis 8637 ORF1023 1096633 1097082 peptidyl-tRNA hydrolase U31570 Chlamydiatrachomatis 378 53 ORF1024 1097266 1097601 ribosomal protein S6 (rps6)AE000630 Helicobacter pylori 179 39 ORF1025 1097622 1097867 ribosomalprotein S18 homolog; putative M62820 Chlamydia trachomatis 324 86ORF1026 1097886 1098392 putative heat shock protein ORF; putative M62820Chlamydia trachomatis 190 79 ORF1027 1099521 1099279 putative ORF10281099689 1101053 putative ORF1029 1102192 1101107 putative ORF10301104950 1102116 glycerol-3-phosphate acyltransferase M80571 Cucumissativus 574 43 ORF1031 1106508 1104946 ORF_f495; orfF of ECMRED, uses2nd start U18997 Escherichia coli 855 38 ORF1032 1106722 1107249putative ORF1033 1107463 1108101 PlsX U59433 Bacillus subtilis 282 45ORF1034 1108041 1108421 fatty acid/phospholipid synthesis proteinAE000540 Helicobacter pylori 205 35 (plsX) ORF1035 1108520 1113370putative 98 kDa outer membrane protein U72499 Chlamydia psittaci 352 44ORF1036 1114958 1113447 putative ORF1037 1116915 1115071 lipid Adisaccharide synthetase (lpxB) U32786 Haemophilus influenzae 477 42ORF1038 1118183 1116894 poly(A) polymerase AE000123 Escherichia coli 55546 ORF1039 1118846 1120030 putative L12968 Escherichia coli 880 50ORF1040 1120040 1120522 glucosamine fructose-6-phosphate AE000651Helicobacter pylori 396 52 aminotransferase (isomerizing) (glmS) ORF10411120510 1121430 glutamine amidotransferase; glucosamine- AE000450Escherichia coli 494 44 fructose-6-phosphate aminotransferase ORF10421121321 1121866 L-glutamine: D-fructose-6-P U17352 Thermus aquaticusthermophilus 374 50 amidotransferase precursor ORF1043 1122123 1122899tyrosine-specific transport protein AE000284 Escherichia coli 281 41ORF1044 1124842 1125564 putative ORF1045 1126526 1125579 cell divisionprotein (ftsY) U32760 Haemophilus influenzae 497 41 ORF1046 11265191127676 succinyl-CoA synthetase beta-subunit J01619 Escherichia coli 78443 ORF1047 1127672 1128571 succinyl coenzyme A synthetase alpha U23408Dictyostelium discoideum 978 63 subunit ORF1048 1130230 1131336 putativeORF1049 1131480 1132553 putative ORF1050 1132830 1133843 putativeORF1051 1134121 1134855 serine protease HtrA D90905 Synechocystis sp.307 51 ORF1052 1134642 1135592 GsrA protein D78376 Yersiniaenterocolitica 497 41 ORF1053 1135964 1135653 putative ORF1054 11371321135954 R11H6.1 Z93386 Caenorhabditis elegans 445 37 ORF1055 11371691140102 Ydr430cp; CAI: 0.15 U33007 Saccharomyces cerevisiae 559 40ORF1056 1141365 1140112 hypothetical 54.7 kD protein in udp 3′ AE000459Escherichia coli 222 34 region precursor (o475) ORF1057 1142150 1141356phosphatidylserine synthase (pssA) AE000614 Helicobacter pylori 307 41ORF1058 1142520 1145660 ribonucleotide reductase subunit M1 K02927 Musmusculus 1433 45 ORF1059 1145627 1146721 ribonucleoside diphosphatereductase, beta AE000553 Helicobacter pylori 443 32 subunit (nrdB)ORF1060 1146862 1147545 unknown Z95398 Mycobacterium leprae 191 35ORF1061 1147666 1148190 YtqB AF008220 Bacillus subtilis 262 44 ORF10621148514 1148224 ORF2 U01958 Bacillus licheniformis 135 54 ORF10631149136 1148348 ORF2 M31827 Bacillus subtilis 268 40 ORF1064 11497021149166 putative ORF1065 1150031 1150591 unknown Z85982 Mycobacteriumtuberculosis 445 49 ORF1066 1150785 1151147 ribosomal protein L20 (AA1–119) X16188 Bacillus stearothermophilus 273 44 ORF1067 1151165 1152181phenylalany-tRNA synthetase beta subunit Z75208 Bacillus subtilis 777 40ORF1068 1152522 1154591 putative ORF1069 1155666 1154566 putativeORF1070 1156743 1155670 putative ORF1071 1156859 1157815 hypotheticalU32723 Haemophilus influenzae 252 42 ORF1072 1157982 1160735 ATP-bindingprotein U01376 Escherichia coli 1314 56 ORF1073 1162620 1160917polynucleotide phosphorylase AF010578 Pisum sativum 1416 52 ORF10741162970 1162590 polyribonucleotide phophorylase U52048 Spinacia oleracea312 53 ORF1075 1163532 1164020 orf150 gene product X95938 Porphyromonasgingivalis 335 43 ORF1076 1163995 1164294 putative ORF1077 11655691165030 putative ORF1078 1166108 1165566 putative ORF1079 11666441166141 putative ORF1080 1167055 1168374 putative ORF1081 11692181168337 methionine aminopeptidase D64003 Synechocystis sp. 488 54ORF1082 1169823 1169218 ORF_o197 U18997 Escherichia coli 281 30 ORF10831171324 1170572 putative ORF1084 1172085 1171177 hypothetical U32720Haemophilus influenzae 162 44 ORF1085 1172394 1173773 fumarase D64000Synechocystis sp. 1292 57 ORF1086 1175209 1173881 prs-associatedputative membrane protein U02424 Escherichia coli 570 39 ORF1087 11755551175127 hypothetical protein in pth-prs intergenic AE000219 Escherichiacoli 278 46 region ORF1088 1175778 1177043 hypothetical protein Z96072Mycobacterium tuberculosis 109 43 ORF1089 1177177 1179048 putativeORF1090 1179156 1180085 penicillin tolerance protein (lytB) U32781Haemophilus influenzae 731 54 ORF1091 1180045 1180779 putative ORF10921181942 1180788 putative ORF1093 1182296 1181961 putative ORF10941183844 1182300 putative ORF1095 1184420 1183848 putative ORF10961185382 1184366 putative ORF1097 1185858 1185226 putative ORF10981186164 1186481 putative ORF1099 1187386 1186484 site-specificrecombinase U92524 Salmonella typhimurium 401 48 ORF1100 1187370 1189028phophoglucoisomerase-like protein L40822 Chlamydia trachomatis 1154 63ORF1101 1189321 1190889 putative ORF1102 1191142 1192146 NADP-malatedehydrogenase L40958 Flaveria bidentis 775 46 ORF1103 1191974 1191729putative ORF1104 1193815 1192991 putative ORF1105 1195702 1194248 o460;This 460 aa orf is 46 pct identical (26 AE000256 Escherichia coli 102244 gaps) to 458 residues of an approx. 488 aa protein ARCD_PSEAE SW:P18275 ORF1106 1196303 1195716 putative ORF1107 1196831 1196337 putativeORF1108 1197807 1196746 putative ORF1109 1198740 1197883 putativeORF1110 1200232 1198721 shikimate 5-dehydrogenase U67551 Methanococcusjannaschii 245 37 ORF1111 1201286 1200135 3-dehydroquinate synthase(aroB) U32705 Haemophilus influenzae 478 45 ORF1112 1202386 12012592,3-dihydroxybenzoic acid L29562 Vibrio anguillarum 780 50 ORF11131202901 1202350 putative ORF1114 1204162 1202816 5-enolpyruvylshikimate3-phosphate U67500 Methanococcus jannaschii 520 40 synthase ORF11151203177 1203464 putative ORF1116 1205028 1204180 putative ORF11171206392 1204878 bioA gene product A02587 unidentified 834 48 ORF11181206742 1206086 dethiobiotin synthase (bioD) U32830 Haemophilusinfluenzae 243 37 ORF1119 1207872 1206724 L-alanine-pimelyl CoA ligaseU51868 Bacillus subtilis 601 41 ORF1120 1208852 1207851 biotin sythaseU24147 Arabidopsis thaliana 892 52 ORF1121 1210518 1209742 tryptophanhydroxylase U26428 Gallus gallus 237 34 ORF1122 1210703 1211494dihydrodipicolinate reductase U47017 Pseudomonas syringae pv. tabaci 34537 ORF1123 1211870 1212754 aspartate-semialdehyde dehydrogenase U67476Methanococcus jannaschii 444 43 ORF1124 1212742 1214064 aspartokinaseIII U00006 Escherichia coli 473 47 ORF1125 1214046 1214858dihydrodipicolinate synthase D64006 Synechocystis sp. 238 40 ORF11261215551 1216318 putative ORF1127 1216493 1216849 putative ORF11281217183 1219612 putative ORF1129 1220068 1219673 putative ORF11301219710 1220669 putative ORF1131 1220630 1221376 putative ORF11321221645 1223681 unknown D26185 Bacillus subtilis 621 43 ORF1133 12238941224988 putative ORF1134 1225000 1225830 high level kasgamycinresistance D26185 Bacillus subtilis 422 41 ORF1135 1227810 1225879hypothetical protein D90903 Synechocystis sp. 1129 43 ORF1136 12265281226908 putative ORF1137 1229972 1228311 exonuclease VII, large subunit(xseA) U32723 Haemophilus influenzae 666 46 ORF1138 47569 47018Integrase/recombinase AE001308 Chlamydia trachomatis 716 72 ORF113949980 49117 putative ORF1140 53356 52898 putative ORF1141 54477 54884O-Sialoglycoprotein Endopeptidase AE001307 Chlamydia trachomatis 311 51ORF1142 63753 63998 PTS PEP Phosphotransferase AE001306 Chlamydiatrachomatis 198 61 ORF1143 77164 77487 putative ORF1144 79724 79302 SmsProtein AE001302 Chlamydia trachomatis 458 57 ORF1145 88721 88951putative ORF1146 94067 94429 putative ORF1147 122832 123341 hypotheticalprotein AE001303 Chlamydia trachomatis 398 61 ORF1148 147536 147234putative ORF1149 158990 159346 S16 Ribosomal Protein AE001277 Chlamydiatrachomatis 467 78 ORF1150 168470 168979 putative ORF1151 169183 169452putative ORF1152 171785 171504 Cationic Amino Acid Transporter AE001278Chlamydia trachomatis 262 68 ORF1153 172518 171775 Cationic Amino AcidTransporter AE001278 Chlamydia trachomatis 533 48 ORF1154 193599 194045putative ORF1155 195704 196075 S/T Protein Kinase AE001288 Chlamydiatrachomatis 536 82 ORF1156 210687 210145 KDO-transferase X80061Chlamydia pneumoniae 856 96 ORF1157 211100 210708 putative ORF1158215420 215088 putative ORF1159 217914 218246 putative ORF1160 218925218701 putative ORF1161 223785 223525 IMP dehydrogenase U13372 Borreliaburgdorferi 270 63 ORF1162 224271 223999 putative ORF1163 228691 228407putative ORF1164 235050 235334 (Methylase) AE001287 Chlamydiatrachomatis 331 66 ORF1165 252308 253021 Oligopeptide Permease AE001293Chlamydia trachomatis 838 72 ORF1166 258280 258912 DicarboxylateTranslocator AE001294 Chlamydia trachomatis 909 80 ORF1167 261325 261567putative ORF1168 268195 268878 hypothetical protein AE001287 Chlamydiatrachomatis 556 52 ORF1169 269447 268881 putative ORF1170 271263 271538putative ORF1171 271957 272346 putative ORF1172 274176 274550 putativeORF1173 275736 275314 Disulfide bond Oxidoreductase AE001291 Chlamydiatrachomatis 519 73 ORF1174 276490 276927 hypothetical protein AE001291Chlamydia trachomatis 249 53 ORF1175 277577 277861 hypothetical proteinAE001291 Chlamydia trachomatis 256 52 ORF1176 288163 287909 putativeORF1177 290130 289789 putative ORF1178 290989 291225 putative ORF1179291372 291860 adenylate cyclase AE001286 Chlamydia trachomatis 388 48ORF1180 311239 311622 putative ORF1181 328665 328384 putative ORF1182337348 338289 sodium-dependent transporter AF017105 Chlamydia psittaci1112 72 ORF1183 364764 364369 Prolipoprotein Diacylglycerol TransferaseAE001298 Chlamydia trachomatis 300 54 ORF1184 389623 390135 hypotheticalprotein AE001282 Chlamydia trachomatis 75 33 ORF1185 393729 394343 ABCsuperfamily ATPase AE001282 Chlamydia trachomatis 473 52 ORF1186 407379407621 putative ORF1187 410944 410708 putative ORF1188 427632 427988putative ORF1189 428172 428486 putative ORF1190 436761 437246hypothetical protein AE001279 Chlamydia trachomatis 661 81 ORF1191460911 461159 putative ORF1192 477597 477313 hypothetical proteinAE001300 Chlamydia trachomatis 309 62 ORF1193 487303 487001 putativeORF1194 487764 487534 Glycine Cleavage System H Protein AE001300Chlamydia trachomatis 221 67 ORF1195 498502 499017 hypothetical proteinAE001275 Chlamydia trachomatis 206 32 ORF1196 499795 500466 putativeORF1197 571928 572344 putative ORF1198 572367 572131 putative ORF1199588184 587915 hypothetical protein AE001312 Chlamydia trachomatis 256 62ORF1200 600587 600907 (Metalloenzyme) AE001316 Chlamydia trachomatis 31461 ORF1201 609731 608895 putative ORF1202 614039 614755 hypotheticalprotein AE001317 Chlamydia trachomatis 475 46 ORF1203 614823 615152putative ORF1204 638244 638831 ABC Transporter ATPase AE001315 Chlamydiatrachomatis 614 61 ORF1205 638819 639094 (Metal Transport Protein)AE001315 Chlamydia trachomatis 265 63 ORF1206 639073 639636 (MetalTransport Protein) AE001315 Chlamydia trachomatis 687 69 ORF1207 647901648236 hypothetical protein AE001317 Chlamydia trachomatis 139 38ORF1208 678510 679469 phosphohydrolase AE001320 Chlamydia trachomatis995 63 ORF1209 688178 688732 hypothetical protein AE001320 Chlamydiatrachomatis 366 43 ORF1210 696045 696563 methyltransferase AE001321Chlamydia trachomatis 369 49 ORF1211 708998 708588 Glucose-1-PAdenyltransferase AE001322 Chlamydia trachomatis 507 83 ORF1212 709808710089 putative ORF1213 718240 717737 Glycerol-3-PPhosphatidyltransferase AE001323 Chlamydia trachomatis 573 66 ORF1214737828 737565 S19 Ribosomal Protein AE001323 Chlamydia trachomatis 43994 ORF1215 779502 780257 hypothetical protein AE001322 Chlamydiatrachomatis 476 48 ORF1216 806310 805864 hypothetical protein AE001337Chlamydia trachomatis 512 67 ORF1217 820931 820707 putative ORF1218837696 839096 Exodeoxyribonuclease V, Gamma AE001334 Chlamydiatrachomatis 967 49 ORF1219 883307 883549 putative ORF1220 892010 891726putative ORF1221 893277 893564 putative ORF1222 936998 937225 Gen.Secretion Protein E AE001327 Chlamydia trachomatis 256 67 ORF1223 946865947419 putative ORF1224 975187 975411 SWF/SNF family helicase AE001341Chlamydia trachomatis 363 96 ORF1225 985882 985517 hypothetical proteinAE001342 Chlamydia trachomatis 166 33 ORF1226 987713 987180 hypotheticalprotein AE001342 Chlamydia trachomatis 447 59 ORF1227 988215 987733Flagellar M-Ring Protein AE001342 Chlamydia trachomatis 304 44 ORF1228988754 988530 Flagellar M-Ring Protein AE001342 Chlamydia trachomatis 9236 ORF1229 992542 992841 hypothetical protein AE001343 Chlamydiatrachomatis 112 39 ORF1230 992759 993067 hypothetical protein AE001343Chlamydia trachomatis 100 32 ORF1231 1004247 1004528 D-Ala/Gly PermeaseAE001344 Chlamydia trachomatis 283 64 ORF1232 1015013 1014294 235aa longhypothetical protein AB009472 Pyrococcus horikoshii 104 54 ORF12331056147 1056545 putative ORF1234 1077682 1078035 predicted disulfidebond isomerase AE001351 Chlamydia trachomatis 233 46 ORF1235 10881211088381 putative ORF1236 1098430 1098852 Predicted Kinase AE001352Chlamydia trachomatis 384 59 ORF1237 1098798 1099319 Predicted KinaseAE001352 Chlamydia trachomatis 322 45 ORF1238 1123198 1123515 TransportPermease AE001354 Chlamydia trachomatis 313 72 ORF1239 1123606 1124256Tyrosine Transport AE001354 Chlamydia trachomatis 577 58 ORF1240 11244531124797 Tyrosine Transport AE001354 Chlamydia trachomatis 323 50 ORF12411129253 1129567 putative ORF1242 1164947 1164474 hypothetical proteinAE001357 Chlamydia trachomatis 412 56 ORF1243 1170457 1170053hypothetical protein AE001358 Chlamydia trachomatis 283 59 ORF12441172342 1171863 ABC transporter permease AE001358 Chlamydia trachomatis457 55 ORF1245 1192155 1192835 putative ORF1246 1192759 1192992 putativeORF1247 1193861 1194142 putative ORF1248 1194036 1193779 (D-Amino AcidDehydrogenase) AE001311 Chlamydia trachomatis 269 79 ORF1249 12097481209053 conserved hypothetical protein AE000958 Archaeoglobus fulgidus121 38 ORF1250 1215111 1215419 putative ORF1251 1216302 1216538 putativeORF1252 1228072 1227818 hypothetical protein AE001306 Chlamydiatrachomatis 134 39 ORF1253 1228304 1228080 xseB AL021897 Mycobacteriumtuberculosis 89 33 ORF1254 26599 26222 putative ORF1255 27609 27367putative ORF1256 67206 66967 putative ORF1257 70612 70352 putativeORF1258 132703 132945 putative ORF1259 178073 178393 putative ORF1260208576 208349 putative ORF1261 209156 208929 putative ORF1262 209263209024 putative ORF1263 210304 210639 putative ORF1264 299009 299452putative ORF1265 352106 351717 putative ORF1266 420182 419949 FlagellarSecretion Protein AE001280 Chlamydia trachomatis 115 43 ORF1267 553602553381 putative ORF1268 556538 556807 putative ORF1269 594348 593797putative ORF1270 595169 594876 putative ORF1271 662148 662381 putativeORF1272 706528 706893 putative ORF1273 803315 803650 putative ORF1274849551 849306 putative ORF1275 913676 913275 putative ORF1276 927087926836 putative ORF1277 930587 930360 putative ORF1278 986531 986764 ORF12 M72718 Bacillus subtilis 106 48 ORF1279 996229 996486 putativeORF1280 1000373 1000002 putative ORF1281 1010291 1010037 putativeORF1282 1011128 1010793 106aa long hypothetical protein AB009472Pyrococcus horikoshii 159 50 ORF1283 1012924 1012694 putative ORF12841028659 1028913 putative ORF1285 1086481 1086762 putative ORF12861118658 1118879 Phosphoglucomutase AE001354 Chlamydia trachomatis 291 84ORF1287 1170098 1169835 hypothetical protein AE001358 Chlamydiatrachomatis 187 53 ORF1288 1180828 1181184 putative ORF1289 11826581183035 putative ORF1290 1195076 1194795 putative ORF1291 11958901196183 putative

TABLE 2 ORF Nos begin end potential start 2 42 794 42 3 1258 1614 1261 41807 2418 1807 5 3393 2491 3393 6 3639 4067 3639 7 5649 4270 5649 8 74636012 7463 9 8051 8962 8051 10 9129 9959 9138 11 10687 10361 10639 1210927 11232 10927 13 11246 12727 11246 14 12691 14190 12691 15 1448417249 14484 16 16039 15770 16036 17 17845 20853 17845 18 21137 2204221137 19 22046 23476 22046 20 23681 26110 23681 21 26109 25861 26109 2226241 26978 26241 23 26960 27754 26960 24 27747 28577 27747 25 2888729492 28950 26 29432 30028 29432 27 30024 31472 30024 28 31758 3228831758 29 32201 33991 32201 30 33852 34541 33852 31 34783 36063 34783 3236009 37529 36009 33 37881 39362 37881 34 39418 39161 39418 35 3936640715 39366 36 43076 41094 43076 37 43800 43066 43800 38 44828 4378544768 39 45340 44753 45340 40 45752 45372 45752 41 46996 45701 46996 4247961 47569 47961 43 48960 48040 48960 44 51452 50133 51452 45 5260651335 52606 46 53684 53319 53684 47 54195 53746 54195 48 55278 5645355278 49 56493 57266 56493 50 57297 58526 57297 51 59851 58565 59851 5261495 59924 61495 53 61324 62151 61324 54 62132 62470 62132 55 6247463733 62474 56 63881 64186 63881 57 64611 64318 64611 58 65485 6467365485 59 65999 65301 65999 60 66244 67281 66244 61 67265 67699 67265 6267703 68539 67760 63 68805 70736 68805 64 69172 68831 69172 65 7064271142 70642 66 71325 72029 71325 67 72060 73637 72060 68 74061 7617574061 69 78351 77680 78351 70 79356 78355 79356 71 79983 79693 79983 7280441 79938 80441 73 80475 80969 80475 74 81296 83080 81332 75 8329183932 83291 76 84005 84769 84005 77 84975 85244 84975 78 85123 8542585123 79 85397 85903 85397 80 85909 86583 85909 81 86626 88065 86626 8289257 91026 89257 83 91291 93030 91291 84 93295 94086 93295 85 9528594707 95279 86 95667 96557 95667 87 96317 97456 96317 88 98435 9796898435 89 99460 98426 99460 90 100144 101325 100144 91 101457 101720101457 92 101704 102273 101704 93 102356 102805 102356 94 102835 103530102835 95 103549 104058 103549 96 104096 104491 104096 97 104601 108386104601 98 108401 112054 108401 99 112033 112590 112033 100 112672 113682112672 101 113726 114121 113726 102 114711 114136 114711 103 115267115755 115267 104 115911 116543 115911 105 116736 118055 116778 106117968 118522 117968 107 118530 119843 118530 108 119816 120457 119816109 120451 122430 120451 110 122504 122950 122504 111 123528 126347123528 112 126332 129166 126332 113 134690 129213 134690 114 134925136382 134931 115 137870 136482 137867 116 137899 138240 137899 117138239 137928 138239 118 139558 138257 139558 119 140352 139516 140352120 140498 141841 140498 121 141855 142658 141855 122 144258 143050144258 123 145258 144494 145258 124 145454 146749 145454 125 147318146767 147318 126 148261 147677 148261 127 149029 152157 149029 128154108 152201 154108 129 155135 154308 155135 130 155141 155467 155141131 155703 156779 155703 132 156748 157635 156748 133 157653 158996157653 134 159363 159986 159363 135 159880 160446 159880 136 160477160839 160477 137 160898 161539 160898 138 161527 162153 161527 139162144 162443 162144 140 162437 164098 162437 141 165451 164228 165451142 166349 165411 166349 143 166949 168442 166949 144 169416 171029169416 145 170857 171459 170857 146 172652 173428 172652 147 174626173439 174626 148 174816 175613 174816 149 175598 175954 175598 150175958 176935 175958 151 177708 176938 177708 152 177128 177376 177128153 179472 177841 179472 154 179822 179517 179822 155 181793 179943181793 156 182628 181876 182628 157 184420 183074 184420 158 184988184467 184988 159 185483 185112 185483 160 185902 185483 185902 161186174 185839 186174 162 187720 186587 187720 163 188318 190933 188318164 191090 191635 191090 165 191547 192743 191547 166 192969 193469192969 167 194044 193610 194044 168 194196 195809 194196 169 196088198073 196088 170 198132 199454 198132 171 199351 202818 199351 172204552 202999 204552 173 205648 204692 205639 174 205807 207327 205807175 207182 207775 207182 176 207779 208267 207779 177 208267 209577208267 178 211807 211271 211807 179 212188 211844 212188 180 214079212448 214079 181 214907 214083 214907 182 216154 215429 216154 183216115 216678 216115 184 216728 217282 216728 185 217267 217866 217267186 218593 218261 218590 187 219821 218994 219821 188 221382 220309221382 189 222719 221433 222719 190 223521 222724 223521 191 224499225008 224499 192 225140 225559 225140 193 225555 226802 225555 194227800 226892 227743 195 228335 228072 228335 196 229251 228643 229251197 230983 229622 230983 198 231483 230983 231483 199 232063 231509232063 200 232739 232053 232739 201 233166 234356 233166 202 233518233165 233518 203 234536 235186 234536 204 235379 236689 235379 205236680 237618 236689 206 237521 238345 237521 207 238281 238973 238281208 238871 240115 238871 209 240191 241564 240191 210 242281 241604242281 211 242933 242274 242933 212 243416 242976 243416 213 243500244531 243500 214 244480 246021 244480 215 246330 247811 246330 216247831 249174 247870 217 249437 251038 249455 218 251325 252212 251325219 253156 254007 253156 220 253974 254852 253974 221 255258 256094255258 222 256640 257455 256640 223 257502 258239 257502 224 257869257501 257869 225 259248 260897 259248 226 262753 261788 262753 227263059 262757 263059 228 264375 263182 264375 229 265985 264747 265985230 266637 266059 266637 231 267338 266538 267338 232 267922 267473267922 233 269647 270771 269647 234 272777 273145 272777 235 273253273636 273253 236 273705 273977 273705 237 276016 275717 276016 238276439 276020 276418 239 276792 277253 276792 240 277318 277599 277318241 278578 277877 278578 242 279258 278554 279258 243 280435 279533280435 244 281547 280849 281547 245 281696 282325 281717 246 282459284069 282459 247 284056 284517 284056 248 284606 285775 284606 249285592 285987 285592 250 286179 286976 286179 251 287583 287002 287583252 287951 287451 287951 253 288499 288816 288499 254 289674 288505289674 255 288839 289213 288839 256 289970 290254 289970 257 291931292803 291931 258 293258 292755 293258 259 293718 293272 293718 260294630 293953 294630 261 296153 294636 296153 262 294817 295068 294817263 296354 297862 296354 264 298415 297879 298415 265 298777 298253298777 266 299572 298781 299572 267 300487 299633 300487 268 301586300702 301568 269 302440 301571 302440 270 302838 302437 302838 271303335 302745 303335 272 304394 303852 304394 273 304606 305223 304606274 305394 306236 305394 275 306501 307439 306501 276 308033 307458308033 277 308924 308037 308924 278 309485 310180 309485 279 310426311214 310426 280 311597 311253 311504 281 312772 311780 312772 282313425 312772 313425 283 313646 313377 313646 284 313937 314665 313937285 315576 314755 315576 286 316157 315531 316157 287 318657 316156318657 288 321042 318676 321042 289 321445 321098 321445 290 322309321710 322309 291 323190 322366 323181 292 323843 323181 323843 293324878 323856 324878 294 325340 326410 325340 295 326433 327836 326433296 328465 327839 328465 297 329360 328857 329360 298 330907 329357330907 299 332455 330956 332455 300 334536 332395 334536 301 336091334877 336091 302 336103 337302 336103 303 338129 338830 338129 304338965 339501 338965 305 339508 340143 339508 306 340247 342967 340247307 343385 343810 343385 308 344171 343935 344171 309 345082 344330345073 310 346005 345082 346005 311 346784 346437 346784 312 347029346715 347029 313 347034 347723 347034 314 348075 350459 348075 315350598 351071 350598 316 351075 352175 351096 317 353291 352230 353267318 353442 354467 353442 319 354451 354933 354451 320 355000 355449355000 321 355448 356743 355448 322 355953 355642 355953 323 359310356827 359310 324 359120 359377 359120 325 359525 359908 359525 326361290 359947 361290 327 363785 361362 363746 328 364496 363888 364496329 364832 365290 364832 330 365304 365669 365304 331 366599 365667366599 332 367291 369030 367291 333 369134 369808 369134 334 369917370438 369917 335 370365 372647 370365 336 372557 373066 372557 337373020 373442 373020 338 373467 374195 373467 339 374176 375099 374176340 375676 375083 375676 341 376173 375634 376173 342 376564 377643376564 343 377956 379773 377956 344 379781 380425 379805 345 380281381000 380281 346 381008 381460 381008 347 381460 383037 381460 348383257 383523 383257 349 383553 385304 383553 350 385397 386458 385400351 387242 386514 387242 352 388764 387013 388764 353 390120 390932390120 354 390919 391818 390961 355 392379 391885 392379 356 392582392986 392582 357 392776 393684 392776 358 394151 394804 394151 359394928 395308 394928 360 395259 395990 395259 361 397815 395953 397815362 398850 397831 398850 363 400085 399099 400085 364 401245 400073401236 365 401474 401136 401474 366 402199 401423 402199 367 403193402186 403166 368 403650 404165 403650 369 404343 405914 404343 370405984 407327 405984 371 407712 408806 407712 372 410439 409075 410439373 411826 410954 411826 374 412482 414302 412482 375 415402 414407415402 376 415848 415237 415848 377 417131 415866 417131 378 417258417566 417258 379 418326 417454 418326 380 420057 418426 420057 381420448 420720 420448 382 420980 421552 420980 383 421556 422029 421556384 422461 422925 422461 385 423562 424320 423562 386 424250 424591424250 387 424830 426047 424830 388 426240 427397 426240 389 428841430703 428841 390 430694 431446 430694 391 431597 432100 431597 392432165 432779 432165 393 433272 432832 433272 394 433925 433227 433922395 436678 433934 436678 396 437176 438357 437176 397 440317 438518440317 398 440001 440345 440001 399 441233 440517 441233 400 440719441012 440719 401 442192 441230 442192 402 442888 442343 442888 403442371 442961 442371 404 443578 443003 443578 405 444500 443526 444500406 444842 444528 444842 407 445009 444743 445009 408 445718 445182445718 409 445807 447804 445807 410 448738 447803 448738 411 449628448618 449628 412 450298 450867 450298 413 450713 451207 450713 414451211 452452 451211 415 452448 453659 452448 416 454843 453725 454843417 455608 454865 455608 418 456243 457007 456243 419 457016 457708457016 420 458368 457979 458368 421 459496 458372 459496 422 459493460194 459493 423 461446 460355 461446 424 462298 461450 462298 425462444 463349 462444 426 464241 463342 464241 427 464574 465065 464574428 465129 465611 465129 429 465571 466317 465571 430 466317 467093466317 431 466999 467502 466999 432 469691 467715 469691 433 470691469660 470691 434 472010 470709 472010 435 471545 471799 471545 436472359 472045 472359 437 473523 472732 473523 438 474889 473441 474889439 477323 475365 477323 440 478496 477597 478496 441 478722 479273478722 442 479277 479705 479277 443 480050 481450 480050 444 481469482053 481469 445 482600 482025 482600 446 482654 484204 482654 447484211 485170 484211 448 485170 485838 485170 449 485813 486580 485813450 486976 486638 486976 451 489071 487764 489071 452 489341 489090489341 453 489958 489152 489958 454 490549 489962 490549 455 491163490522 491163 456 491396 491112 491396 457 492121 491390 492121 458492304 494838 492304 459 495943 494822 495943 460 496011 496565 496170461 496569 497228 496569 462 497358 497834 497358 463 497770 498327497770 464 499209 499589 499209 465 499520 499792 499520 466 500774504169 500774 467 504139 504600 504139 468 504865 506877 504865 469506790 507671 506790 470 507718 510507 507718 471 508325 507912 508325472 510660 513440 510660 473 514965 513787 514920 474 517347 515419517347 475 517058 517363 517058 476 517798 517277 517798 477 518200517847 518200 478 518300 521146 518363 479 521392 522948 521407 480523244 524809 523322 481 524379 524125 524379 482 524649 526238 524649483 526265 527104 526268 484 526947 526702 526947 485 526975 528450526975 486 528408 529199 528408 487 530612 529542 530612 488 531656530616 531656 489 533974 532067 533974 490 536432 534324 536432 491537150 536707 537150 492 537928 537080 537928 493 538438 537932 538438494 538737 538333 538737 495 539594 539127 539594 496 541215 539590541215 497 542571 541282 542571 498 543014 542457 543014 499 543369542962 543369 500 543809 546628 543815 501 546619 549525 546619 502547293 546994 547293 503 549699 550523 549699 504 550490 551551 550490505 551448 552623 551448 506 552652 555117 552652 507 555029 555493555029 508 558006 555673 558006 509 559694 558162 559694 510 558208558573 558208 511 561692 559899 561692 512 561412 561708 561412 513563942 561777 563942 514 564969 563950 564969 515 566204 564936 566198516 567717 566302 567717 517 568526 567708 568526 518 569467 568742569467 519 571065 569431 571065 520 571828 571118 571783 521 572202573308 572202 522 573146 575056 573146 523 575023 575916 575023 524577891 576497 577891 525 578914 578204 578914 526 579924 578857 579924527 580187 579858 580187 528 580017 580406 580017 529 581086 580187581086 530 581367 581828 581367 531 581678 582367 581678 532 582361583428 582361 533 584690 583431 584690 534 585237 584950 585237 535585626 586888 585626 536 586846 587907 586888 537 589049 588180 589049538 590500 589301 590455 539 590755 592458 590755 540 592526 592903592526 541 592836 593747 592836 542 593747 594298 593747 543 594331595947 594331 544 595905 596309 595905 545 596514 597215 596514 546597184 597957 597184 547 597755 598612 597755 548 598602 599204 598602549 599373 599939 599373 550 600903 602072 600903 551 602240 602587602240 552 602637 603272 602637 553 603142 604512 603142 554 604627605853 604627 555 605790 606620 605790 556 606571 607281 606571 557609004 607355 609004 558 610906 609932 610906 559 611786 611004 611786560 612333 611746 612333 561 613897 612341 613897 562 615179 616279615179 563 616610 617383 616610 564 618796 617810 618796 565 620004618826 620004 566 619649 619918 619649 567 621265 620021 621265 568622359 621265 622359 569 623420 622560 623420 570 624297 623335 624297571 624773 624174 624773 572 625029 625484 625029 573 625488 625883625488 574 625892 626395 625892 575 626444 627790 626444 576 627912628607 627930 577 628774 629697 628774 578 629660 631639 629660 579631725 633551 631725 580 633520 636957 633520 581 637232 638098 637232582 640648 639593 640648 583 640979 640728 640979 584 641327 641007641327 585 641687 642283 641687 586 643023 642286 643023 587 643330643076 643330 588 643704 643351 643704 589 645628 643676 645628 590645783 645538 645756 591 646269 645793 646269 592 646751 646314 646751593 647848 647045 647848 594 648393 650336 648393 595 651016 650420651007 596 652956 651289 652956 597 653395 653126 653395 598 655740654193 655740 599 656508 655966 656508 600 658140 657022 658140 601660216 658525 660216 602 663238 660248 663238 603 664461 663157 664452604 665735 664635 665735 605 666212 666994 666212 606 666998 667921666998 607 667909 668568 667909 608 668502 669203 668502 609 669154670893 669175 610 672226 670853 672226 611 671137 671424 671137 612672453 673001 672453 613 673072 674721 673072 614 674549 674262 674549615 675518 674796 675518 616 676083 675499 676083 617 676630 676067676630 618 677016 676600 677016 619 677647 677015 677647 620 677990678259 677990 621 679444 680097 679444 622 680097 680897 680097 623681637 680849 681637 624 681409 682281 681409 625 682453 682821 682453626 682763 683902 682763 627 684616 683969 684616 628 685169 684534685169 629 685986 685117 685986 630 686278 687288 686278 631 687483688151 687483 632 688740 689501 688740 633 690242 689622 690242 634690470 691126 690470 635 692600 691497 692600 636 692674 695064 692674637 695049 696032 695064 638 697964 696585 697964 639 699803 698274699803 640 701926 699788 701926 641 703196 702567 703196 642 704221703208 704221 643 704240 705289 704240 644 706070 705300 706070 645706841 706254 706838 646 707596 706811 707596 647 708666 707677 708666648 709793 709119 709793 649 711523 710132 711523 650 712236 711523712236 651 714734 712125 714734 652 715759 714761 715759 653 717538715886 717538 654 719113 720243 719113 655 720590 722422 720590 656722406 723056 722406 657 723551 723120 723551 658 724246 723626 724246659 724754 724251 724754 660 725868 724900 725868 661 727115 726270727115 662 728126 727119 728126 663 728594 728208 728594 664 729614728604 729614 665 729778 729533 729778 666 730149 729751 730149 667730539 730174 730539 668 731983 730598 731983 669 732427 731996 732427670 732917 732423 732917 671 733598 733320 733598 672 733869 733492733869 673 734298 733900 734298 674 734858 734319 734858 675 735195734863 735195 676 735578 735342 735578 677 735861 735604 735861 678736492 736079 736492 679 737192 736524 737192 680 737555 737211 737555681 738688 737837 738688 682 739048 738713 739048 683 739736 739065739736 684 740477 739773 740477 685 740659 740958 740659 686 741722740721 741722 687 742789 741827 742789 688 743618 742782 743618 689744092 743634 744092 690 744604 744107 744604 691 744953 744498 744953692 746608 744986 746608 693 747085 746621 747085 694 747974 747219747974 695 748594 748169 748594 696 749145 748573 749145 697 749652749957 749652 698 750446 749979 750446 699 751219 750446 751219 700753042 751291 753042 701 754309 753020 754309 702 755120 756175 755120703 756120 756485 756120 704 756499 760227 756499 705 761217 760297761178 706 761297 761809 761330 707 761782 762282 761782 708 762260762895 762299 709 762867 763316 762867 710 763780 763325 763780 711763861 765168 763861 712 766809 765697 766809 713 768051 766888 768051714 768566 768321 768566 715 769342 768551 769342 716 770532 769378770532 717 771451 770804 771451 718 773058 771847 773058 719 773094773456 773094 720 774376 773093 774376 721 775123 774380 775123 722775398 774916 775398 723 775046 776077 775046 724 776070 777041 776070725 777964 777536 777964 726 778176 777904 778176 727 778621 779334778684 728 781173 780307 781173 729 781526 781116 781526 730 782784781555 782784 731 783572 782805 783572 732 785032 783581 785032 733786412 785360 786412 734 788429 786450 788429 735 788944 788528 788944736 789758 788901 789758 737 790332 791504 790338 738 791846 792721791846 739 792724 793569 792724 740 793580 794323 793580 741 794304794843 794304 742 795217 795732 795217 743 795722 796795 795722 744798735 797053 798735 745 799823 798681 799823 746 799297 799578 799297747 801313 799808 801313 748 802453 801332 802453 749 803299 802457803299 750 803811 803290 803811 751 805151 803826 805151 752 805860805156 805860 753 806604 806332 806604 754 806913 806608 806913 755808222 806903 808222 756 808751 808146 808751 757 809437 808673 809437758 809939 809454 809939 759 811235 810213 811235 760 811779 813056811779 761 812890 812516 812890 762 812954 813583 812954 763 813587815023 813587 764 815420 815746 815420 765 816036 817010 816036 766817111 817356 817111 767 817791 818609 817797 768 818609 819094 818609769 819104 819823 819104 770 820722 819826 820722 771 822313 821000822313 772 823503 822238 823503 773 823678 825612 823678 774 825461826312 825461 775 827280 826645 827280 776 828604 827171 828604 777830026 828713 830026 778 831047 830085 831047 779 831725 831051 831725780 832220 833098 832220 781 833851 833396 833851 782 834068 835039834068 783 835792 835127 835792 784 837624 836116 837624 785 838951840882 838951 786 840869 842185 840869 787 841989 843455 841989 788843242 844021 843242 789 845018 843987 844997 790 846174 844990 846174791 848509 846311 848509 792 848568 849014 848568 793 849082 850488849088 794 851512 850574 851512 795 852064 852447 852064 796 852398853690 852398 797 855118 854243 855118 798 855751 855128 855751 799856551 855829 856551 800 856730 858556 856730 801 858717 859601 858717802 859591 860205 859591 803 861132 860284 861132 804 861426 861163861426 805 861701 862921 861701 806 863026 864798 863026 807 864831865256 864831 808 865226 866581 865226 809 866562 867119 866562 810867025 867816 867025 811 867820 868497 867820 812 869743 868661 869743813 870633 870094 870633 814 871929 870646 871929 815 872538 872086872538 816 873908 872517 873908 817 874281 874670 874281 818 874582875286 874582 819 877857 875377 877857 820 878446 879255 878446 821880635 879268 880635 822 882524 880593 882524 823 882612 883319 882612824 884155 883538 884155 825 884340 885611 884343 826 885722 887302885722 827 887587 888153 887587 828 888627 888220 888627 829 889330888716 889330 830 889898 889323 889898 831 891190 889898 891190 832891828 891247 891828 833 892421 892017 892421 834 893116 892421 893116835 892521 892925 892521 836 893392 895419 893392 837 895745 896527895745 838 896668 897558 896668 839 897565 899442 897565 840 899420900229 899420 841 903230 900237 903230 842 905081 903234 905081 843906931 905045 906931 844 907248 907832 907299 845 907784 908128 907784846 908132 908677 908132 847 908589 909320 908589 848 909405 911465909405 849 911677 912360 911725 850 912303 912821 912303 851 912937913983 912937 852 915128 914067 915128 853 916658 915303 916658 854915627 915376 915627 855 917707 916853 917707 856 918837 917722 918837857 919868 918837 919868 858 920434 919880 920434 859 921187 920438921187 860 921959 921195 921959 861 923773 921995 923773 862 922146922415 922146 863 923943 923674 923943 864 924077 925006 924077 865925436 925083 925436 866 926524 925349 926524 867 927920 926433 927920868 928319 927951 928319 869 928963 928334 928963 870 929248 930987929248 871 930995 932059 930995 872 932121 933515 932175 873 932881932513 932881 874 933485 935746 933485 875 935724 937082 935724 876937229 938410 937229 877 938281 938805 938281 878 938809 939255 938824879 939165 939782 939165 880 939760 940791 939790 881 940822 941106940822 882 940977 941351 940977 883 942537 941623 942429 884 942784942500 942763 885 943149 942799 943149 886 943799 943029 943799 887944055 943732 944055 888 944413 943994 944404 889 945395 944556 945395890 945853 945389 945853 891 946392 945751 946392 892 947410 948081947431 893 949871 948915 949871 894 951058 949868 951058 895 951249950959 951249 896 951664 952134 951664 897 952674 952165 952674 898953491 952589 953491 899 955324 953495 955324 900 955823 955281 955823901 957082 955847 957082 902 957902 957270 957902 903 959231 957906959231 904 959376 960284 959376 905 960266 961669 960347 906 961856964765 961856 907 966855 965395 966855 908 968204 966975 968204 909968791 968237 968791 910 969498 968731 969498 911 969858 969511 969858912 970118 969762 970118 913 970593 970300 970593 914 971261 970542971261 915 971680 971123 971680 916 971876 975100 971876 917 975419976516 975419 918 976584 978320 976584 919 977680 977231 977680 920978399 980738 978399 921 980756 981928 980756 922 982974 981931 982962923 984120 983119 984120 924 985502 984120 985502 925 987180 985882987180 926 987172 987444 987172 927 989846 989049 989846 928 991048989846 991048 929 991638 990955 991638 930 991794 992498 991794 931993619 993041 993619 932 993530 994792 993548 933 995970 994795 995970934 996857 995739 996857 935 997603 996782 997603 936 998969 997572998969 937 998896 1000023 998896 938 1000087 1001340 1000087 939 10013571001818 1001357 940 1003288 1001873 1003288 941 1003487 1004146 1003496942 1004485 1005639 1004689 943 1005643 1005972 1005643 944 10067841006116 1006784 945 1007563 1006769 1007563 946 1009226 1007568 1009226947 1009989 1009336 1009989 948 1015852 1016337 1015852 949 10165611016181 1016561 950 1016297 1017532 1016297 951 1016802 1016452 1016802952 1018993 1017701 1018993 953 1019454 1019137 1019454 954 10207641019562 1020764 955 1021405 1021037 1021405 956 1021821 1024286 1021821957 1024697 1024248 1024697 958 1025569 1024508 1025551 959 10269691025590 1026969 960 1027789 1026947 1027789 961 1031199 1027945 1031199962 1031717 1031172 1031717 963 1033057 1031612 1033057 964 10334251033039 1033425 965 1033784 1033200 1033784 966 1033963 1036038 1033963967 1036945 1036010 1036945 968 1037110 1037679 1037110 969 10376961037944 1037696 970 1038916 1037975 1038916 971 1040582 1039026 1040582972 1040997 1042337 1040997 973 1042357 1043403 1042357 974 10433671044623 1043367 975 1044607 1045362 1044607 976 1045384 1046538 1045384977 1046447 1047517 1046447 978 1047521 1049956 1047521 979 10506111050036 1050611 980 1050925 1050566 1050925 981 1051728 1051090 1051728982 1051743 1052063 1051743 983 1052101 1053126 1052101 984 10542011053107 1054201 985 1054242 1055555 1054242 986 1055483 1055908 1055483987 1056609 1056965 1056609 988 1056961 1058232 1056985 989 10582381058687 1058238 990 1059371 1058727 1059371 991 1059526 1060578 1059526992 1061553 1060579 1061553 993 1061674 1062411 1061674 994 10623771064077 1062377 995 1064116 1065243 1064116 996 1067451 1065178 1067451997 1068065 1067376 1068065 998 1068209 1068706 1068230 999 10699581068819 1069958 1000 1071163 1070033 1071163 1001 1072438 10713321072438 1002 1072997 1073476 1072997 1003 1074239 1075864 1074239 10041076790 1075867 1076790 1005 1077268 1076573 1077268 1006 10779991078724 1077999 1007 1079088 1078672 1079088 1008 1079642 10799441079642 1009 1080501 1079995 1080468 1010 1080775 1081341 1080775 10111083158 1081350 1083158 1012 1084677 1083235 1084677 1013 10856481084632 1085648 1014 1086117 1086737 1086117 1015 1086692 10878971086692 1016 1088646 1089005 1088646 1017 1089146 1089805 1089146 10181092931 1089890 1092931 1019 1093179 1092889 1093179 1020 10935841094204 1093584 1021 1095619 1094192 1095619 1022 1096074 10966281096074 1023 1096633 1097082 1096633 1024 1097266 1097601 1097266 10251097622 1097867 1097622 1026 1097886 1098392 1097886 1027 10995211099279 1099521 1028 1099689 1101053 1099704 1029 1102192 11011071102192 1030 1104950 1102116 1104950 1031 1106508 1104946 1106508 10321106722 1107249 1106722 1033 1107463 1108101 1107463 1034 11080411108421 1108041 1035 1108520 1113370 1108520 1036 1114958 11134471114958 1037 1116915 1115071 1116915 1038 1118183 1116894 1118183 10391118846 1120030 1118846 1040 1120040 1120522 1120040 1041 11205101121430 1120510 1042 1121321 1121866 1121321 1043 1122123 11228991122123 1044 1124842 1125564 1124842 1045 1126526 1125579 1126526 10461126519 1127676 1126519 1047 1127672 1128571 1127672 1048 11302301131336 1130230 1049 1131480 1132553 1131480 1050 1132830 11338431132830 1051 1134121 1134855 1134121 1052 1134642 1135592 1134642 10531135964 1135653 1135964 1054 1137132 1135954 1137132 1055 11371691140102 1137169 1056 1141365 1140112 1141344 1057 1142150 11413561142150 1058 1142520 1145660 1142520 1059 1145627 1146721 1145627 10601146862 1147545 1146862 1061 1147666 1148190 1147666 1062 11485141148224 1148514 1063 1149136 1148348 1149136 1064 1149702 11491661149702 1065 1150031 1150591 1150031 1066 1150785 1151147 1150785 10671151165 1152181 1151165 1068 1152522 1154591 1152522 1069 11556661154566 1155666 1070 1156743 1155670 1156740 1071 1156859 11578151156859 1072 1157982 1160735 1157982 1073 1162620 1160917 1162620 10741162970 1162590 1162970 1075 1163532 1164020 1163532 1076 11639951164294 1163995 1077 1165569 1165030 1165569 1078 1166108 11655661166108 1079 1166644 1166141 1166644 1080 1167055 1168374 1167055 10811169218 1168337 1169218 1082 1169823 1169218 1169823 1083 11713241170572 1171324 1084 1172085 1171177 1172085 1085 1172394 11737731172394 1086 1175209 1173881 1175209 1087 1175555 1175127 1175360 10881175778 1177043 1175778 1089 1177177 1179048 1177177 1090 11791561180085 1179156 1091 1180045 1180779 1180045 1092 1181942 11807881181942 1093 1182296 1181961 1182296 1094 1183844 1182300 1183844 10951184420 1183848 1184420 1096 1185382 1184366 1185382 1097 11858581185226 1185858 1098 1186164 1186481 1186185 1099 1187386 11864841187386 1100 1187370 1189028 1187370 1101 1189321 1190889 1189321 11021191142 1192146 1191142 1103 1191974 1191729 1191974 1104 11938151192991 1193815 1105 1195702 1194248 1195702 1106 1196303 11957161196303 1107 1196831 1196337 1196831 1108 1197807 1196746 1197651 11091198740 1197883 1198668 1110 1200232 1198721 1200232 1111 12012861200135 1201286 1112 1202386 1201259 1202350 1113 1202901 12023501202901 1114 1204162 1202816 1204162 1115 1203177 1203464 1203177 11161205028 1204180 1205028 1117 1206392 1204878 1206392 1118 12067421206086 1206742 1119 1207872 1206724 1207872 1120 1208852 12078511208852 1121 1210518 1209742 1210518 1122 1210703 1211494 1210703 11231211870 1212754 1211870 1124 1212742 1214064 1212742 1125 12140461214858 1214046 1126 1215551 1216318 1215551 1127 1216493 12168491216493 1128 1217183 1219612 1217183 1129 1220068 1219673 1220068 11301219710 1220669 1219710 1131 1220630 1221376 1220630 1132 12216451223681 1221645 1133 1223894 1224988 1223900 1134 1225000 12258301225000 1135 1227810 1225879 1227810 1136 1226528 1226908 1226528 11371229972 1228311 1229972 1138 47569 47018 47569 1139 49980 49117 499801140 53356 52898 53356 1141 54477 54884 54477 1142 63753 63998 637531143 77164 77487 77164 1144 79724 79302 79724 1145 88721 88951 887211146 94067 94429 94067 1147 122832 123341 122832 1148 147536 147234147536 1149 158990 159346 158990 1150 168470 168979 168470 1151 169183169452 169204 1152 171785 171504 171785 1153 172518 171775 172518 1154193599 194045 193599 1155 195704 196075 195704 1156 210687 210145 2106841157 211100 210708 211100 1158 215420 215088 215420 1159 217914 218246217914 1160 218925 218701 218925 1161 223785 223525 223785 1162 224271223999 224271 1163 228691 228407 228691 1164 235050 235334 235050 1165252308 253021 252308 1166 258280 258912 258280 1167 261325 261567 2613251168 268195 268878 268195 1169 269447 268881 269447 1170 271263 271538271263 1171 271957 272346 271957 1172 274176 274550 274176 1173 275736275314 275736 1174 276490 276927 276490 1175 277577 277861 277577 1176288163 287909 288163 1177 290130 289789 290130 1178 290989 291225 2909891179 291372 291860 291372 1180 311239 311622 311239 1181 328665 328384328665 1182 337348 338289 337348 1183 364764 364369 364764 1184 389623390135 389623 1185 393729 394343 393729 1186 407379 407621 407379 1187410944 410708 410944 1188 427632 427988 427632 1189 428172 428486 4281721190 436761 437246 436761 1191 460911 461159 460911 1192 477597 477313477597 1193 487303 487001 487303 1194 487764 487534 487764 1195 498502499017 498502 1196 499795 500466 499795 1197 571928 572344 571928 1198572367 572131 572367 1199 588184 587915 588184 1200 600587 600907 6005871201 609731 608895 609731 1202 614039 614755 614039 1203 614823 615152614823 1204 638244 638831 638244 1205 638819 639094 638819 1206 639073639636 639073 1207 647901 648236 647901 1208 678510 679469 678510 1209688178 688732 688178 1210 696045 696563 696045 1211 708998 708588 7089981212 709808 710089 709808 1213 718240 717737 718240 1214 737828 737565737828 1215 779502 780257 779502 1216 806310 805864 806310 1217 820931820707 820931 1218 837696 839096 837696 1219 883307 883549 883307 1220892010 891726 892010 1221 893277 893564 893277 1222 936998 937225 9369981223 946865 947419 946865 1224 975187 975411 975187 1225 985882 985517985882 1226 987713 987180 987713 1227 988215 987733 988215 1228 988754988530 988754 1229 992542 992841 992542 1230 992759 993067 992759 12311004247 1004528 1004268 1232 1015013 1014294 1015013 1233 10561471056545 1056147 1234 1077682 1078035 1077682 1235 1088121 10883811088121 1236 1098430 1098852 1098430 1237 1098798 1099319 1098798 12381123198 1123515 1123198 1239 1123606 1124256 1123606 1240 11244531124797 1124453 1241 1129253 1129567 1129253 1242 1164947 11644741164947 1243 1170457 1170053 1170457 1244 1172342 1171863 1172342 12451192155 1192835 1192155 1246 1192759 1192992 1192759 1247 11938611194142 1193861 1248 1194036 1193779 1194036 1249 1209748 12090531209748 1250 1215111 1215419 1215111 1251 1216302 1216538 1216302 12521228072 1227818 1228072 1253 1228304 1228080 1228304 1254 26599 2622226599 1255 27609 27367 27609 1256 67206 66967 67197 1257 70612 7035270588 1258 132703 132945 132703 1259 178073 178393 178073 1260 208576208349 208576 1261 209156 208929 209156 1262 209263 209024 209263 1263210304 210639 210304 1264 299009 299452 299030 1265 352106 351717 3520611266 420182 419949 420170 1267 553602 553381 553602 1268 556538 556807556538 1269 594348 593797 594342 1270 595169 594876 595160 1271 662148662381 662160 1272 706528 706893 706528 1273 803315 803650 803339 1274849551 849306 849551 1275 913676 913275 913676 1276 927087 926836 9270871277 930587 930360 930587 1278 986531 986764 986531 1279 996229 996486996229 1280 1000373 1000002 1000334 1281 1010291 1010037 1010273 12821011128 1010793 1011128 1283 1012924 1012694 1012924 1284 10286591028913 1028659 1285 1086481 1086762 1086481 1286 1118658 11188791118658 1287 1170098 1169835 1170098 1288 1180828 1181184 1180828 12891182658 1183035 1182658 1290 1195076 1194795 1195055 1291 11958901196183 1195890 1292 189042 188809 189030 1293 691250 691567 691250 1294914544 914780 914556 1295 928525 928833 928579 1296 1040685 10409481040712 1297 377646 378068 377646

TABLE 3 ORF 25, ORF 26, ORF 27; ORF 28, ORF 29, ORF 30; ORF 31, ORF 32;ORF 33, ORF 35; ORF 466, ORF 467; ORF 468, ORF 469; ORF 477, ORF 476,ORF 474; ORF 480, ORF 482; ORF 483, ORF 485, ORF 486, ORF 500; ORF 503,ORF 504, ORF 505; ORF 506, ORF 507; ORF 1211, ORF 647; ORF 1286, ORF1039; ORF 691, ORF 690; ORF 105, ORF 106; ORF 170, ORF 171; ORF 394, ORF393; ORF 453, ORF 452, ORF 451; ORF 526, ORF 525; ORF 757, ORF 756, ORF755; ORF 856, ORF 855; ORF 958, ORF 957; ORF 915, ORF 914, ORF 913; ORF543, ORF 544; ORF 1266, ORF 380; ORF 745, ORF 744; ORF 777, ORF 776; ORF343, ORF 1297, and representative fragments.

TABLE 4 SEQ ID NO (ORF) Fp Fd Bp Bd 2 1292 1293 3796 3797 3 1294 12953798 3799 4 1296 1297 3800 3801 5 1298 1299 3802 3803 6 1300 1301 38043805 7 1302 1303 3806 3807 8 1304 1305 3808 3809 9 1306 1307 3810 381110 1308 1309 3812 3813 11 1310 1311 3814 3815 12 1312 1313 3816 3817 131314 1315 3818 3819 14 1316 1317 3820 3821 15 1318 1319 3822 3823 161320 1321 3824 3825 17 1322 1323 3826 3827 18 1324 1325 3828 3829 191326 1327 3830 3831 20 1328 1329 3832 3833 21 1330 1331 3834 3835 221332 1333 3836 3837 23 1334 1335 3838 3839 24 1336 1337 3840 3841 251338 1339 3842 3843 26 1340 1341 3844 3845 27 1342 1343 3846 3847 281344 1345 3848 3849 29 1346 1347 3850 3851 30 1348 1349 3852 3853 311350 1351 3854 3855 32 1352 1353 3856 3857 33 1354 1355 3858 3859 341358 1359 3862 3863 35 1356 1357 3860 3861 36 1360 1361 3864 3865 371362 1363 3866 3867 38 1364 1365 3868 3869 39 1366 1367 3870 3871 401368 1369 3872 3873 41 1370 1371 3874 3875 42 1374 1375 3878 3879 431376 1377 3880 3881 44 1380 1381 3884 3885 45 1382 1383 3886 3887 461386 1387 3890 3891 47 1388 1389 3892 3893 48 1392 1393 3896 3897 491394 1395 3898 3899 50 1396 1397 3900 3901 51 1398 1399 3902 3903 521402 1403 3906 3907 53 1400 1401 3904 3905 54 1404 1405 3908 3909 551406 1407 3910 3911 56 1410 1411 3914 3915 57 1412 1413 3916 3917 581414 1415 3918 3919 59 1416 1417 3920 3921 60 1418 1419 3922 3923 611420 1421 3924 3925 62 1422 1423 3926 3927 63 1424 1425 3928 3929 641426 1427 3930 3931 65 1428 1429 3932 3933 66 1430 1431 3934 3935 671432 1433 3936 3937 68 1434 1435 3938 3939 69 1438 1439 3942 3943 701440 1441 3944 3945 71 1444 1445 3948 3949 72 1446 1447 3950 3951 731448 1449 3952 3953 74 1450 1451 3954 3955 75 1452 1453 3956 3957 761454 1455 3958 3959 77 1456 1457 3960 3961 78 1458 1459 3962 3963 791460 1461 3964 3965 80 1462 1463 3966 3967 81 1464 1465 3968 3969 821468 1469 3972 3973 83 1470 1471 3974 3975 84 1472 1473 3976 3977 851476 1477 3980 3981 86 1478 1479 3982 3983 87 1480 1481 3984 3985 881482 1483 3986 3987 89 1484 1485 3988 3989 90 1486 1487 3990 3991 911488 1489 3992 3993 92 1490 1491 3994 3995 93 1492 1493 3996 3997 941494 1495 3998 3999 95 1496 1497 4000 4001 96 1498 1499 4002 4003 971500 1501 4004 4005 98 1502 1503 4006 4007 99 1504 1505 4008 4009 1001506 1507 4010 4011 101 1508 1509 4012 4013 102 1510 1511 4014 4015 1031512 1513 4016 4017 104 1514 1515 4018 4019 105 1516 1517 4020 4021 1061518 1519 4022 4023 107 1520 1521 4024 4025 108 1522 1523 4026 4027 1091524 1525 4028 4029 110 1526 1527 4030 4031 111 1530 1531 4034 4035 1121532 1533 4036 4037 113 1534 1535 4038 4039 114 1536 1537 4040 4041 1151538 1539 4042 4043 116 1540 1541 4044 4045 117 1542 1543 4046 4047 1181544 1545 4048 4049 119 1546 1547 4050 4051 120 1548 1549 4052 4053 1211550 1551 4054 4055 122 1552 1553 4056 4057 123 1554 1555 4058 4059 1241556 1557 4060 4061 125 1558 1559 4062 4063 126 1562 1563 4066 4067 1271564 1565 4068 4069 128 1566 1567 4070 4071 129 1568 1569 4072 4073 1301570 1571 4074 4075 131 1572 1573 4076 4077 132 1574 1575 4078 4079 1331576 1577 4080 4081 134 1580 1581 4084 4085 135 1582 1583 4086 4087 1361584 1585 4088 4089 137 1586 1587 4090 4091 138 1588 1589 4092 4093 1391590 1591 4094 4095 140 1592 1593 4096 4097 141 1594 1595 4098 4099 1421596 1597 4100 4101 143 1598 1599 4102 4103 144 1604 1605 4108 4109 1451606 1607 4110 4111 146 1612 1613 4116 4117 147 1614 1615 4118 4119 1481616 1617 4120 4121 149 1618 1619 4122 4123 150 1620 1621 4124 4125 1511624 1625 4128 4129 152 1622 1623 4126 4127 153 1626 1627 4130 4131 1541628 1629 4132 4133 155 1630 1631 4134 4135 156 1632 1633 4136 4137 1571634 1635 4138 4139 158 1636 1637 4140 4141 159 1638 1639 4142 4143 1601640 1641 4144 4145 161 1642 1643 4146 4147 162 1644 1645 4148 4149 1631646 1647 4150 4151 164 1648 1649 4152 4153 165 1650 1651 4154 4155 1661652 1653 4156 4157 167 1656 1657 4160 4161 168 1658 1659 4162 4163 1691662 1663 4166 4167 170 1664 1665 4168 4169 171 1666 1667 4170 4171 1721668 1669 4172 4173 173 1670 1671 4174 4175 174 1672 1673 4176 4177 1751674 1675 4178 4179 176 1676 1677 4180 4181 177 1678 1679 4182 4183 1781684 1685 4188 4189 179 1686 1687 4190 4191 180 1688 1689 4192 4193 1811690 1691 4194 4195 182 1694 1695 4198 4199 183 1696 1697 4200 4201 1841698 1699 4202 4203 185 1700 1701 4204 4205 186 1704 1705 4208 4209 1871708 1709 4212 4213 188 1710 1711 4214 4215 189 1712 1713 4216 4217 1901714 1715 4218 4219 191 1720 1721 4224 4225 192 1722 1723 4226 4227 1931724 1725 4228 4229 194 1726 1727 4230 4231 195 1728 1729 4232 4233 1961732 1733 4236 4237 197 1734 1735 4238 4239 198 1736 1737 4240 4241 1991738 1739 4242 4243 200 1740 1741 4244 4245 201 1742 1743 4246 4247 2021744 1745 4248 4249 203 1746 1747 4250 4251 204 1750 1751 4254 4255 2051752 1753 4256 4257 206 1754 1755 4258 4259 207 1756 1757 4260 4261 2081758 1759 4262 4263 209 1760 1761 4264 4265 210 1762 1763 4266 4267 2111764 1765 4268 4269 212 1766 1767 4270 4271 213 1768 1769 4272 4273 2141770 1771 4274 4275 215 1772 1773 4276 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9313338 3339 5842 5843 932 3336 3337 5840 5841 933 3340 3341 5844 5845 9343342 3343 5846 5847 935 3344 3345 5848 5849 936 3346 3347 5850 5851 9373348 3349 5852 5853 938 3350 3351 5854 5855 939 3352 3353 5856 5857 9403354 3355 5858 5859 941 3356 3357 5860 5861 942 3360 3361 5864 5865 9433362 3363 5866 5867 944 3364 3365 5868 5869 945 3366 3367 5870 5871 9463368 3369 5872 5873 947 3370 3371 5874 5875 948 3374 3375 5878 5879 9493378 3379 5882 5883 950 3376 3377 5880 5881 951 3380 3381 5884 5885 9523382 3383 5886 5887 953 3384 3385 5888 5889 954 3386 3387 5890 5891 9553388 3389 5892 5893 956 3390 3391 5894 5895 957 3392 3393 5896 5897 9583394 3395 5898 5899 959 3396 3397 5900 5901 960 3398 3399 5902 5903 9613400 3401 5904 5905 962 3402 3403 5906 5907 963 3404 3405 5908 5909 9643406 3407 5910 5911 965 3408 3409 5912 5913 966 3410 3411 5914 5915 9673412 3413 5916 5917 968 3414 3415 5918 5919 969 3416 3417 5920 5921 9703418 3419 5922 5923 971 3420 3421 5924 5925 972 3422 3423 5926 5927 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6014 6015 1015 3512 3513 6016 6017 1016 3516 3517 6020 60211017 3518 3519 6022 6023 1018 3520 3521 6024 6025 1019 3522 3523 60266027 1020 3524 3525 6028 6029 1021 3526 3527 6030 6031 1022 3528 35296032 6033 1023 3530 3531 6034 6035 1024 3532 3533 6036 6037 1025 35343535 6038 6039 1026 3536 3537 6040 6041 1027 3542 3543 6046 6047 10283544 3545 6048 6049 1029 3546 3547 6050 6051 1030 3548 3549 6052 60531031 3550 3551 6054 6055 1032 3552 3553 6056 6057 1033 3554 3555 60586059 1034 3556 3557 6060 6061 1035 3558 3559 6062 6063 1036 3560 35616064 6065 1037 3562 3563 6066 6067 1038 3564 3565 6068 6069 1039 35663567 6070 6071 1040 3568 3569 6072 6073 1041 3570 3571 6074 6075 10423572 3573 6076 6077 1043 3574 3575 6078 6079 1044 3582 3583 6086 60871045 3584 3585 6088 6089 1046 3586 3587 6090 6091 1047 3588 3589 60926093 1048 3592 3593 6096 6097 1049 3594 3595 6098 6099 1050 3596 35976100 6101 1051 3598 3599 6102 6103 1052 3600 3601 6104 6105 1053 36023603 6106 6107 1054 3604 3605 6108 6109 1055 3606 3607 6110 6111 10563608 3609 6112 6113 1057 3610 3611 6114 6115 1058 3612 3613 6116 61171059 3614 3615 6118 6119 1060 3616 3617 6120 6121 1061 3618 3619 61226123 1062 3620 3621 6124 6125 1063 3622 3623 6126 6127 1064 3624 36256128 6129 1065 3626 3627 6130 6131 1066 3628 3629 6132 6133 1067 36303631 6134 6135 1068 3632 3633 6136 6137 1069 3634 3635 6138 6139 10703636 3637 6140 6141 1071 3638 3639 6142 6143 1072 3640 3641 6144 61451073 3642 3643 6146 6147 1074 3644 3645 6148 6149 1075 3646 3647 61506151 1076 3648 3649 6152 6153 1077 3652 3653 6156 6157 1078 3654 36556158 6159 1079 3656 3657 6160 6161 1080 3658 3659 6162 6163 1081 36603661 6164 6165 1082 3662 3663 6166 6167 1083 3666 3667 6170 6171 10843668 3669 6172 6173 1085 3672 3673 6176 6177 1086 3674 3675 6178 61791087 3676 3677 6180 6181 1088 3678 3679 6182 6183 1089 3680 3681 61846185 1090 3682 3683 6186 6187 1091 3684 3685 6188 6189 1092 3686 36876190 6191 1093 3688 3689 6192 6193 1094 3690 3691 6194 6195 1095 36923693 6196 6197 1096 3694 3695 6198 6199 1097 3696 3697 6200 6201 10983698 3699 6202 6203 1099 3702 3703 6206 6207 1100 3700 3701 6204 62051101 3704 3705 6208 6209 1102 3706 3707 6210 6211 1103 3708 3709 62126213 1104 3714 3715 6218 6219 1105 3720 3721 6224 6225 1106 3722 37236226 6227 1107 3724 3725 6228 6229 1108 3726 3727 6230 6231 1109 37283729 6232 6233 1110 3730 3731 6234 6235 1111 3732 3733 6236 6237 11123734 3735 6238 6239 1113 3736 3737 6240 6241 1114 3740 3741 6244 62451115 3738 3739 6242 6243 1116 3742 3743 6246 6247 1117 3744 3745 62486249 1118 3746 3747 6250 6251 1119 3748 3749 6252 6253 1120 3750 37516254 6255 1121 3754 3755 6258 6259 1122 3756 3757 6260 6261 1123 37583759 6262 6263 1124 3760 3761 6264 6265 1125 3762 3763 6266 6267 11263766 3767 6270 6271 1127 3770 3771 6274 6275 1128 3772 3773 6276 62771129 3776 3777 6280 6281 1130 3774 3775 6278 6279 1131 3778 3779 62826283 1132 3780 3781 6284 6285 1133 3782 3783 6286 6287 1134 3784 37856288 6289 1135 3788 3789 6292 6293 1136 3786 3787 6290 6291 1137 37943795 6298 6299 1138 1372 1373 3876 3877 1139 1378 1379 3882 3883 11401384 1385 3888 3889 1141 1390 1391 3894 3895 1142 1408 1409 3912 39131143 1436 1437 3940 3941 1144 1442 1443 3946 3947 1145 1466 1467 39703971 1146 1474 1475 3978 3979 1147 1528 1529 4032 4033 1148 1560 15614064 4065 1149 1578 1579 4082 4083 1150 1600 1601 4104 4105 1151 16021603 4106 4107 1152 1608 1609 4112 4113 1153 1610 1611 4114 4115 11541654 1655 4158 4159 1155 1660 1661 4164 4165 1156 1680 1681 4184 41851157 1682 1683 4186 4187 1158 1692 1693 4196 4197 1159 1702 1703 42064207 1160 1706 1707 4210 4211 1161 1716 1717 4220 4221 1162 1718 17194222 4223 1163 1730 1731 4234 4235 1164 1748 1749 4252 4253 1165 17801781 4284 4285 1166 1794 1795 4298 4299 1167 1798 1799 4302 4303 11681814 1815 4318 4319 1169 1816 1817 4320 4321 1170 1820 1821 4324 43251171 1822 1823 4326 4327 1172 1830 1831 4334 4335 1173 1832 1833 43364337 1174 1838 1839 4342 4343 1175 1844 1845 4348 4349 1176 1870 18714374 4375 1177 1880 1881 4384 4385 1178 1882 1883 4386 4387 1179 18841885 4388 4389 1180 1932 1933 4436 4437 1181 1968 1969 4472 4473 11821982 1983 4486 4487 1183 2036 2037 4540 4541 1184 2086 2087 4590 45911185 2098 2099 4602 4603 1186 2126 2127 4630 4631 1187 2132 2133 46364637 1188 2166 2167 4670 4671 1189 2168 2169 4672 4673 1190 2184 21854688 4689 1191 2240 2241 4744 4745 1192 2276 2277 4780 4781 1193 23002301 4804 4805 1194 2302 2303 4806 4807 1195 2330 2331 4834 4835 11962336 2337 4840 4841 1197 2448 2449 4952 4953 1198 2452 2453 4956 49571199 2484 2485 4988 4989 1200 2512 2513 5016 5017 1201 2530 2531 50345035 1202 2540 2541 5044 5045 1203 2542 2543 5046 5047 1204 2584 25855088 5089 1205 2586 2587 5090 5091 1206 2588 2589 5092 5093 1207 26142615 5118 5119 1208 2670 2671 5174 5175 1209 2694 2695 5198 5199 12102708 2709 5212 5213 1211 2730 2731 5234 5235 1212 2734 2735 5238 52391213 2746 2747 5250 5251 1214 2802 2803 5306 5307 1215 2898 2899 54025403 1216 2950 2951 5454 5455 1217 2988 2989 5492 5493 1218 3018 30195522 5523 1219 3098 3099 5602 5603 1220 3118 3119 5622 5623 1221 31263127 5630 5631 1222 3208 3209 5712 5713 1223 3242 3243 5746 5747 12243294 3295 5798 5799 1225 3312 3313 5816 5817 1226 3318 3319 5822 58231227 3320 3321 5824 5825 1228 3322 3323 5826 5827 1229 3332 3333 58365837 1230 3334 3335 5838 5839 1231 3358 3359 5862 5863 1232 3372 33735876 5877 1233 3452 3453 5956 5957 1234 3492 3493 5996 5997 1235 35143515 6018 6019 1236 3538 3539 6042 6043 1237 3540 3541 6044 6045 12383576 3577 6080 6081 1239 3578 3579 6082 6083 1240 3580 3581 6084 60851241 3590 3591 6094 6095 1242 3650 3651 6154 6155 1243 3664 3665 61686169 1244 3670 3671 6174 6175 1245 3710 3711 6214 6215 1246 3712 37136216 6217 1247 3716 3717 6220 6221 1248 3718 3719 6222 6223 1249 37523753 6256 6257 1250 3764 3765 6268 6269 1251 3768 3769 6272 6273 12523790 3791 6294 6295 1253 3792 3793 6296 6297 1254 6300 6301 6376 63771255 6302 6303 6378 6379 1256 6304 6305 6380 6381 1257 6306 6307 63826383 1258 6308 6309 6384 6385 1259 6310 6311 6386 6387 1260 6312 63136388 6389 1261 6314 6315 6390 6391 1262 6316 6317 6392 6393 1263 63186319 6394 6395 1264 6320 6321 6396 6397 1265 6322 6323 6398 6399 12666324 6325 6400 6401 1267 6326 6327 6402 6403 1268 6328 6329 6404 64051269 6330 6331 6406 6407 1270 6332 6333 6408 6409 1271 6334 6335 64106411 1272 6336 6337 6412 6413 1273 6338 6339 6414 6415 1274 6340 63416416 6417 1275 6342 6343 6418 6419 1276 6344 6345 6420 6421 1277 63466347 6422 6423 1278 6348 6349 6424 6425 1279 6350 6351 6426 6427 12806352 6353 6428 6429 1281 6354 6355 6430 6431 1282 6356 6357 6432 64331283 6358 6359 6434 6435 1284 6360 6361 6436 6437 1285 6362 6363 64386439 1286 6364 6365 6440 6441 1287 6366 6367 6442 6443 1288 6368 63696444 6445 1289 6370 6371 6446 6447 1290 6372 6373 6448 6449 1291 63746375 6450 6451

SEQ ID or. 5′position 1292 F 1229848 1293 F 1227874 1294 F 1018 1295 F1229162 1296 F 1588 1297 F 1229711 1298 F 2253 1299 F 369 1300 F 33811301 F 1508 1302 F 4042 1303 F 2126 1304 F 5735 1305 F 3843 1306 F 78321307 F 5909 1308 F 8887 1309 F 7010 1310 F 10139 1311 F 8175 1312 F10640 1313 F 8799 1314 F 10997 1315 F 9037 1316 F 12458 1317 F 105721318 F 14187 1319 F 12365 1320 F 15529 1321 F 13629 1322 F 17626 1323 F15699 1324 F 20909 1325 F 19006 1326 F 21800 1327 F 19927 1328 F 234621329 F 21557 1330 F 25637 1331 F 23729 1332 F 25997 1333 F 24071 1334 F26727 1335 F 24828 1336 F 27528 1337 F 25628 1338 F 28643 1339 F 267651340 F 29202 1341 F 27313 1342 F 29793 1343 F 27835 1344 F 31488 1345 F29639 1346 F 31957 1347 F 30050 1348 F 33570 1349 F 31666 1350 F 345641351 F 32664 1352 F 35783 1353 F 33875 1354 F 37597 1355 F 35741 1356 F39135 1357 F 37236 1358 F 38939 1359 F 37038 1360 F 40872 1361 F 389721362 F 42825 1363 F 40923 1364 F 43563 1365 F 41652 1366 F 44531 1367 F42623 1368 F 45150 1369 F 43250 1370 F 45478 1371 F 43579 1372 F 467551373 F 44874 1374 F 47347 1375 F 45386 1376 F 47818 1377 F 45897 1378 F48893 1379 F 46995 1380 F 49907 1381 F 48000 1382 F 51088 1383 F 491691384 F 52651 1385 F 50721 1386 F 53065 1387 F 51176 1388 F 53516 1389 F51611 1390 F 54242 1391 F 52351 1392 F 55058 1393 F 53159 1394 F 562741395 F 54348 1396 F 57078 1397 F 55156 1398 F 58343 1399 F 56392 1400 F61103 1401 F 59177 1402 F 59701 1403 F 57802 1404 F 61887 1405 F 599711406 F 62255 1407 F 60348 1408 F 63515 1409 F 61557 1410 F 63657 1411 F61761 1412 F 64088 1413 F 62196 1414 F 64422 1415 F 62537 1416 F 650721417 F 63140 1418 F 65978 1419 F 64088 1420 F 67046 1421 F 65146 1422 F67466 1423 F 65580 1424 F 68569 1425 F 66686 1426 F 68609 1427 F 666881428 F 70423 1429 F 68479 1430 F 71099 1431 F 69206 1432 F 71829 1433 F69935 1434 F 73745 1435 F 71931 1436 F 76942 1437 F 75022 1438 F 774041439 F 75556 1440 F 78133 1441 F 76192 1442 F 79079 1443 F 77122 1444 F79471 1445 F 77481 1446 F 79670 1447 F 77816 1448 F 80236 1449 F 783561450 F 81108 1451 F 79182 1452 F 83024 1453 F 81158 1454 F 83786 1455 F81886 1456 F 84739 1457 F 82821 1458 F 84866 1459 F 82967 1460 F 851751461 F 83240 1462 F 85690 1463 F 83790 1464 F 86397 1465 F 84507 1466 F88470 1467 F 86563 1468 F 89038 1469 F 87121 1470 F 91017 1471 F 891461472 F 93075 1473 F 91147 1474 F 93846 1475 F 91948 1476 F 94410 1477 F92561 1478 F 95447 1479 F 93541 1480 F 96074 1481 F 94197 1482 F 977061483 F 95841 1484 F 98142 1485 F 96292 1486 F 99925 1487 F 98011 1488 F101229 1489 F 99338 1490 F 101429 1491 F 99552 1492 F 102137 1493 F100237 1494 F 102600 1495 F 100657 1496 F 103330 1497 F 101429 1498 F103877 1499 F 101966 1500 F 104336 1501 F 102469 1502 F 108182 1503 F106280 1504 F 111814 1505 F 109911 1506 F 112412 1507 F 110553 1508 F113442 1509 F 111571 1510 F 113891 1511 F 112010 1512 F 114990 1513 F113112 1514 F 115684 1515 F 113776 1516 F 116526 1517 F 114656 1518 F117731 1519 F 115825 1520 F 118292 1521 F 116389 1522 F 119593 1523 F117685 1524 F 120231 1525 F 118292 1526 F 122278 1527 F 120382 1528 F122610 1529 F 120682 1530 F 123309 1531 F 121390 1532 F 126113 1533 F124213 1534 F 128975 1535 F 127091 1536 F 134603 1537 F 132806 1538 F136249 1539 F 134352 1540 F 137680 1541 F 135756 1542 F 137680 1543 F135799 1544 F 138035 1545 F 136135 1546 F 139266 1547 F 137363 1548 F140208 1549 F 138351 1550 F 141636 1551 F 139735 1552 F 142808 1553 F140900 1554 F 144272 1555 F 142372 1556 F 145217 1557 F 143335 1558 F146527 1559 F 144645 1560 F 146965 1561 F 145086 1562 F 147455 1563 F145501 1564 F 148810 1565 F 146904 1566 F 151964 1567 F 150062 1568 F154064 1569 F 152113 1570 F 154888 1571 F 152963 1572 F 155418 1573 F153558 1574 F 156528 1575 F 154606 1576 F 157433 1577 F 155516 1578 F158771 1579 F 156842 1580 F 159105 1581 F 157219 1582 F 159657 1583 F157761 1584 F 160240 1585 F 158316 1586 F 160675 1587 F 158778 1588 F161289 1589 F 159402 1590 F 161918 1591 F 159979 1592 F 162214 1593 F160297 1594 F 163996 1595 F 162045 1596 F 165189 1597 F 163288 1598 F166730 1599 F 164828 1600 F 168243 1601 F 166327 1602 F 168907 1603 F167064 1604 F 169129 1605 F 167294 1606 F 170632 1607 F 168692 1608 F171229 1609 F 169381 1610 F 171553 1611 F 169614 1612 F 172433 1613 F170533 1614 F 173217 1615 F 171316 1616 F 174567 1617 F 172680 1618 F175342 1619 F 173479 1620 F 175709 1621 F 173752 1622 F 176909 1623 F175009 1624 F 176704 1625 F 174761 1626 F 177608 1627 F 175709 1628 F179259 1629 F 177384 1630 F 179719 1631 F 177800 1632 F 181629 1633 F179743 1634 F 182851 1635 F 180952 1636 F 184230 1637 F 182335 1638 F184870 1639 F 182962 1640 F 185241 1641 F 183348 1642 F 185611 1643 F183685 1644 F 186336 1645 F 184445 1646 F 188059 1647 F 186171 1648 F190828 1649 F 188956 1650 F 191294 1651 F 189428 1652 F 192686 1653 F190788 1654 F 193380 1655 F 191474 1656 F 193388 1657 F 191474 1658 F193977 1659 F 192059 1660 F 195480 1661 F 193585 1662 F 195868 1663 F193969 1664 F 197913 1665 F 196013 1666 F 199088 1667 F 197213 1668 F202776 1669 F 200876 1670 F 204467 1671 F 202497 1672 F 205584 1673 F203664 1674 F 206940 1675 F 205063 1676 F 207560 1677 F 205587 1678 F208048 1679 F 206139 1680 F 209923 1681 F 208023 1682 F 210455 1683 F208569 1684 F 211049 1685 F 209147 1686 F 211596 1687 F 209705 1688 F212226 1689 F 210311 1690 F 213832 1691 F 211960 1692 F 214866 1693 F212921 1694 F 215173 1695 F 213307 1696 F 215800 1697 F 213957 1698 F216489 1699 F 214549 1700 F 216980 1701 F 215100 1702 F 217665 1703 F215793 1704 F 218039 1705 F 216071 1706 F 218476 1707 F 216560 1708 F218769 1709 F 216809 1710 F 220020 1711 F 218128 1712 F 221210 1713 F219275 1714 F 222497 1715 F 220601 1716 F 223292 1717 F 221403 1718 F223775 1719 F 221877 1720 F 224250 1721 F 222377 1722 F 224906 1723 F223008 1724 F 225283 1725 F 223418 1726 F 226670 1727 F 224770 1728 F227849 1729 F 225937 1730 F 228185 1731 F 226269 1732 F 228393 1733 F226512 1734 F 229334 1735 F 227499 1736 F 230761 1737 F 228846 1738 F231287 1739 F 229334 1740 F 231731 1741 F 229927 1742 F 232865 1743 F231027 1744 F 232865 1745 F 231027 1746 F 234315 1747 F 232394 1748 F234823 1749 F 232865 1750 F 235154 1751 F 233245 1752 F 236429 1753 F234520 1754 F 237268 1755 F 235271 1756 F 238047 1757 F 236162 1758 F238636 1759 F 236736 1760 F 239957 1761 F 238047 1762 F 241373 1763 F239482 1764 F 242017 1765 F 240072 1766 F 242740 1767 F 240829 1768 F243281 1769 F 241373 1770 F 244244 1771 F 242345 1772 F 246052 1773 F244179 1774 F 247581 1775 F 245697 1776 F 249216 1777 F 247244 1778 F251003 1779 F 249137 1780 F 252064 1781 F 250189 1782 F 252900 1783 F251000 1784 F 253718 1785 F 251855 1786 F 254993 1787 F 253138 1788 F256414 1789 F 254509 1790 F 257283 1791 F 255383 1792 F 257279 1793 F255379 1794 F 258061 1795 F 256107 1796 F 259005 1797 F 257128 1798 F261075 1799 F 259195 1800 F 261551 1801 F 259650 1802 F 262535 1803 F260611 1804 F 262960 1805 F 261060 1806 F 264509 1807 F 262614 1808 F265837 1809 F 263925 1810 F 266239 1811 F 264367 1812 F 267185 1813 F265286 1814 F 267909 1815 F 266037 1816 F 268594 1817 F 266756 1818 F269299 1819 F 267505 1820 F 271044 1821 F 269121 1822 F 271737 1823 F269838 1824 F 272558 1825 F 270645 1826 F 273007 1827 F 271098 1828 F273463 1829 F 271500 1830 F 273922 1831 F 272057 1832 F 275083 1833 F273094 1834 F 275495 1835 F 273554 1836 F 275739 1837 F 273878 1838 F276229 1839 F 274371 1840 F 276548 1841 F 274638 1842 F 277098 1843 F275178 1844 F 277358 1845 F 275448 1846 F 277609 1847 F 275739 1848 F278314 1849 F 276386 1850 F 279310 1851 F 277385 1852 F 280627 1853 F278702 1854 F 281471 1855 F 279559 1856 F 282239 1857 F 280288 1858 F283832 1859 F 281933 1860 F 284384 1861 F 282486 1862 F 285373 1863 F283473 1864 F 285919 1865 F 284059 1866 F 286742 1867 F 284879 1868 F287216 1869 F 285329 1870 F 287671 1871 F 285751 1872 F 288273 1873 F286323 1874 F 288618 1875 F 286685 1876 F 288273 1877 F 286323 1878 F289723 1879 F 287836 1880 F 289508 1881 F 287667 1882 F 290750 1883 F288858 1884 F 291142 1885 F 289253 1886 F 291702 1887 F 289812 1888 F292522 1889 F 290633 1890 F 293035 1891 F 291142 1892 F 293731 1893 F291786 1894 F 294530 1895 F 292670 1896 F 294367 1897 F 292513 1898 F296092 1899 F 294209 1900 F 297611 1901 F 295757 1902 F 298027 1903 F296092 1904 F 298555 1905 F 296582 1906 F 299403 1907 F 297511 1908 F300409 1909 F 298579 1910 F 301332 1911 F 299433 1912 F 302215 1913 F300282 1914 F 302492 1915 F 300618 1916 F 303627 1917 F 301730 1918 F304350 1919 F 302487 1920 F 305173 1921 F 303226 1922 F 306244 1923 F304350 1924 F 307232 1925 F 305310 1926 F 307799 1927 F 305877 1928 F309173 1929 F 307301 1930 F 310158 1931 F 308306 1932 F 311020 1933 F309118 1934 F 311031 1935 F 309126 1936 F 311552 1937 F 309658 1938 F312510 1939 F 310614 1940 F 313134 1941 F 311255 1942 F 313674 1943 F311717 1944 F 314490 1945 F 312633 1946 F 315306 1947 F 313355 1948 F315932 1949 F 314033 1950 F 318434 1951 F 316516 1952 F 320876 1953 F318949 1954 F 321403 1955 F 319547 1956 F 322084 1957 F 320217 1958 F322911 1959 F 321049 1960 F 323634 1961 F 321726 1962 F 325117 1963 F323211 1964 F 326213 1965 F 324254 1966 F 327607 1967 F 325695 1968 F328162 1969 F 326262 1970 F 328630 1971 F 326723 1972 F 329134 1973 F327178 1974 F 330734 1975 F 328810 1976 F 332123 1977 F 330252 1978 F334575 1979 F 332660 1980 F 335884 1981 F 333980 1982 F 337129 1983 F335202 1984 F 337910 1985 F 335955 1986 F 338746 1987 F 336795 1988 F339217 1989 F 337362 1990 F 339999 1991 F 338083 1992 F 343144 1993 F341266 1994 F 343699 1995 F 341813 1996 F 344108 1997 F 342204 1998 F344851 1999 F 342933 2000 F 346148 2001 F 344219 2002 F 346493 2003 F344590 2004 F 346815 2005 F 344907 2006 F 347836 2007 F 345956 2008 F350379 2009 F 348432 2010 F 350856 2011 F 348951 2012 F 352008 2013 F350106 2014 F 353209 2015 F 351305 2016 F 354224 2017 F 352312 2018 F354781 2019 F 352871 2020 F 355223 2021 F 353261 2022 F 355393 2023 F353519 2024 F 358901 2025 F 357001 2026 F 356594 2027 F 354692 2028 F359240 2029 F 357374 2030 F 359721 2031 F 357763 2032 F 361071 2033 F359240 2034 F 363605 2035 F 361731 2036 F 364142 2037 F 362246 2038 F364567 2039 F 362708 2040 F 365039 2041 F 363184 2042 F 365445 2043 F363517 2044 F 367040 2045 F 365144 2046 F 368825 2047 F 366993 2048 F369698 2049 F 367760 2050 F 370141 2051 F 368239 2052 F 372329 2053 F370375 2054 F 372779 2055 F 370881 2056 F 373223 2057 F 371342 2058 F373939 2059 F 372017 2060 F 374849 2061 F 372953 2062 F 375351 2063 F373487 2064 F 376316 2065 F 374416 2066 F 377737 2067 F 375828 2068 F379537 2069 F 377660 2070 F 380033 2071 F 378160 2072 F 380789 2073 F378889 2074 F 381238 2075 F 379279 2076 F 382969 2077 F 381124 2078 F383293 2079 F 381425 2080 F 385178 2081 F 383278 2082 F 386271 2083 F384392 2084 F 386780 2085 F 384891 2086 F 389383 2087 F 387504 2088 F389901 2089 F 388001 2090 F 390700 2091 F 388732 2092 F 391612 2093 F389763 2094 F 392346 2095 F 390463 2096 F 392540 2097 F 390639 2098 F393487 2099 F 391609 2100 F 393904 2101 F 392025 2102 F 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B 1002146 5854 B 1001594 5855B 1003567 5856 B 1002100 5857 B 1003941 5858 B 1003571 5859 B 10054125860 B 1004381 5861 B 1006269 5862 B 1004753 5863 B 1006691 5864 B1005890 5865 B 1007762 5866 B 1006199 5867 B 1008109 5868 B 1007050 5869B 1008929 5870 B 1007819 5871 B 1009683 5872 B 1009446 5873 B 10113655874 B 1010314 5875 B 1012109 5876 B 1015234 5877 B 1017133 5878 B1016571 5879 B 1018486 5880 B 1017755 5881 B 1019661 5882 B 1016781 5883B 1018708 5884 B 1017022 5885 B 1018924 5886 B 1019233 5887 B 10211435888 B 1019674 5889 B 1021630 5890 B 1021020 5891 B 1022923 5892 B1021630 5893 B 1023525 5894 B 1024510 5895 B 1026410 5896 B 1024936 5897B 1026858 5898 B 1025836 5899 B 1027677 5900 B 1027197 5901 B 10290895902 B 1028022 5903 B 1029936 5904 B 1031445 5905 B 1033319 5906 B1031943 5907 B 1033839 5908 B 1033277 5909 B 1035186 5910 B 1033697 5911B 1035554 5912 B 1034009 5913 B 1035943 5914 B 1036282 5915 B 10381615916 B 1037178 5917 B 1039088 5918 B 1037902 5919 B 1039802 5920 B1038167 5921 B 1040079 5922 B 1039198 5923 B 1041036 5924 B 1040803 5925B 1042721 5926 B 1042560 5927 B 1044460 5928 B 1043630 5929 B 10455265930 B 1044850 5931 B 1046748 5932 B 1045609 5933 B 1047551 5934 B1046761 5935 B 1048677 5936 B 1047741 5937 B 1049700 5938 B 1050218 5939B 1052151 5940 B 1050831 5941 B 1052744 5942 B 1051223 5943 B 10530715944 B 1051974 5945 B 1053854 5946 B 1052287 5947 B 1054238 5948 B1053379 5949 B 1055253 5950 B 1054458 5951 B 1056325 5952 B 1055816 5953B 1057680 5954 B 1056172 5955 B 1058031 5956 B 1056825 5957 B 10587105958 B 1057197 5959 B 1059089 5960 B 1058522 5961 B 1060355 5962 B1058919 5963 B 1060810 5964 B 1059646 5965 B 1061521 5966 B 1060801 5967B 1062701 5968 B 1061774 5969 B 1063687 5970 B 1062682 5971 B 10645555972 B 1064300 5973 B 1066236 5974 B 1065489 5975 B 1067386 5976 B1067725 5977 B 1069601 5978 B 1068285 5979 B 1070188 5980 B 1068930 5981B 1070898 5982 B 1070188 5983 B 1072078 5984 B 1071383 5985 B 10732835986 B 1072658 5987 B 1074584 5988 B 1073699 5989 B 1075652 5990 B1076111 5991 B 1077988 5992 B 1077010 5993 B 1078959 5994 B 1077598 5995B 1079390 5996 B 1078260 5997 B 1080217 5998 B 1078959 5999 B 10808696000 B 1079354 6001 B 1081215 6002 B 1080217 6003 B 1082067 6004 B1080742 6005 B 1082621 6006 B 1081580 6007 B 1083489 6008 B 1083400 6009B 1085290 6010 B 1084927 6011 B 1086797 6012 B 1085868 6013 B 10877686014 B 1086965 6015 B 1088872 6016 B 1088185 6017 B 1090076 6018 B1088704 6019 B 1090504 6020 B 1089236 6021 B 1091181 6022 B 1090076 6023B 1091944 6024 B 1093259 6025 B 1095056 6026 B 1093403 6027 B 10953016028 B 1094437 6029 B 1096375 6030 B 1095839 6031 B 1097798 6032 B1096858 6033 B 1098751 6034 B 1097305 6035 B 1099205 6036 B 1097835 6037B 1099724 6038 B 1098097 6039 B 1100046 6040 B 1098615 6041 B 11005616042 B 1099098 6043 B 1100975 6044 B 1099614 6045 B 1101442 6046 B1099747 6047 B 1101651 6048 B 1101298 6049 B 1103227 6050 B 1102435 6051B 1104381 6052 B 1105179 6053 B 1107090 6054 B 1106770 6055 B 11086316056 B 1107502 6057 B 1109392 6058 B 1108337 6059 B 1110240 6060 B1108653 6061 B 1110570 6062 B 1113632 6063 B 1115499 6064 B 1115225 6065B 1117081 6066 B 1117154 6067 B 1119051 6068 B 1118403 6069 B 11203106070 B 1120257 6071 B 1122178 6072 B 1120776 6073 B 1122682 6074 B1121660 6075 B 1123554 6076 B 1122120 6077 B 1123999 6078 B 1123243 6079B 1125024 6080 B 1123752 6081 B 1125688 6082 B 1124484 6083 B 11263606084 B 1125020 6085 B 1126928 6086 B 1125790 6087 B 1127735 6088 B1126747 6089 B 1128662 6090 B 1127899 6091 B 1129808 6092 B 1128819 6093B 1130695 6094 B 1129798 6095 B 1131693 6096 B 1131563 6097 B 11334906098 B 1132846 6099 B 1134684 6100 B 1134070 6101 B 1136016 6102 B1135089 6103 B 1137037 6104 B 1135815 6105 B 1137715 6106 B 1136186 6107B 1138084 6108 B 1137365 6109 B 1139255 6110 B 1140364 6111 B 11422286112 B 1141611 6113 B 1143485 6114 B 1142478 6115 B 1144291 6116 B1145907 6117 B 1147783 6118 B 1146953 6119 B 1148846 6120 B 1147769 6121B 1149703 6122 B 1148415 6123 B 1150357 6124 B 1148758 6125 B 11506586126 B 1149462 6127 B 1151258 6128 B 1149932 6129 B 1151845 6130 B1150814 6131 B 1152747 6132 B 1151409 6133 B 1153285 6134 B 1152540 6135B 1154341 6136 B 1154863 6137 B 1156751 6138 B 1155886 6139 B 11578136140 B 1156963 6141 B 1158871 6142 B 1158093 6143 B 1159947 6144 B1160998 6145 B 1162864 6146 B 1162864 6147 B 1164740 6148 B 1163244 6149B 1165090 6150 B 1164244 6151 B 1166175 6152 B 1164517 6153 B 11664826154 B 1165167 6155 B 1167100 6156 B 1165789 6157 B 1167710 6158 B1166376 6159 B 1168228 6160 B 1166872 6161 B 1168764 6162 B 1168598 6163B 1170498 6164 B 1169447 6165 B 1171347 6166 B 1170043 6167 B 11719476168 B 1170689 6169 B 1172616 6170 B 1171556 6171 B 1173507 6172 B1172305 6173 B 1174210 6174 B 1172562 6175 B 1174508 6176 B 1174018 6177B 1175899 6178 B 1175429 6179 B 1177348 6180 B 1175793 6181 B 11776756182 B 1177347 6183 B 1179199 6184 B 1179316 6185 B 1181171 6186 B1180309 6187 B 1182212 6188 B 1181048 6189 B 1182918 6190 B 1182162 6191B 1184078 6192 B 1182528 6193 B 1184437 6194 B 1184078 6195 B 11860156196 B 1184698 6197 B 1186540 6198 B 1185631 6199 B 1187530 6200 B1186079 6201 B 1188004 6202 B 1186704 6203 B 1188610 6204 B 1189251 6205B 1191165 6206 B 1187609 6207 B 1189506 6208 B 1191165 6209 B 11930506210 B 1192378 6211 B 1194291 6212 B 1192265 6213 B 1194114 6214 B1193058 6215 B 1194987 6216 B 1193224 6217 B 1195115 6218 B 1194035 6219B 1195955 6220 B 1194384 6221 B 1196265 6222 B 1194291 6223 B 11962056224 B 1195955 6225 B 1197863 6226 B 1196570 6227 B 1198423 6228 B1197051 6229 B 1198951 6230 B 1198058 6231 B 1199931 6232 B 1198960 6233B 1200867 6234 B 1200490 6235 B 1202395 6236 B 1201512 6237 B 12034266238 B 1202606 6239 B 1204532 6240 B 1203139 6241 B 1205063 6242 B1203691 6243 B 1205597 6244 B 1204382 6245 B 1206284 6246 B 1205249 6247B 1207170 6248 B 1206651 6249 B 1208536 6250 B 1206976 6251 B 12088626252 B 1208092 6253 B 1210002 6254 B 1209115 6255 B 1210973 6256 B1209979 6257 B 1211892 6258 B 1210739 6259 B 1212639 6260 B 1211761 6261B 1213680 6262 B 1212985 6263 B 1214894 6264 B 1214299 6265 B 12161896266 B 1215132 6267 B 1217036 6268 B 1215714 6269 B 1217542 6270 B1216541 6271 B 1218462 6272 B 1216828 6273 B 1218677 6274 B 1217166 6275B 1218973 6276 B 1219876 6277 B 1221743 6278 B 1220892 6279 B 12228956280 B 1220288 6281 B 1222189 6282 B 1221657 6283 B 1223517 6284 B1223930 6285 B 1225828 6286 B 1225211 6287 B 1227132 6288 B 1226090 6289B 1227979 6290 B 1227132 6291 B 1229039 6292 B 1228061 6293 B 12299486294 B 1228293 6295 B 267 6296 B 1228524 6297 B 444 6298 B 267 6299 B2068 6300 F 25997 6301 F 24032 6302 F 27128 6303 F 25189 6304 F 667446305 F 64845 6306 F 70130 6307 F 68200 6308 F 132477 6309 F 130559 6310F 177854 6311 F 175906 6312 F 208127 6313 F 206180 6314 F 208688 6315 F206807 6316 F 208732 6317 F 206877 6318 F 210051 6319 F 208141 6320 F298801 6321 F 296907 6322 F 351495 6323 F 349572 6324 F 419727 6325 F417822 6326 F 553133 6327 F 551247 6328 F 556301 6329 F 554410 6330 F593567 6331 F 591675 6332 F 594641 6333 F 592748 6334 F 661934 6335 F660041 6336 F 706309 6337 F 704409 6338 F 803092 6339 F 801192 6340 F849060 6341 F 847142 6342 F 913050 6343 F 911152 6344 F 926614 6345 F924714 6346 F 930121 6347 F 928238 6348 F 986297 6349 F 984362 6350 F996001 6351 F 994109 6352 F 999731 6353 F 997877 6354 F 1009782 6355 F1007891 6356 F 1010540 6357 F 1008671 6358 F 1012465 6359 F 1010540 6360F 1028431 6361 F 1026524 6362 F 1086215 6363 F 1084362 6364 F 11184176365 F 1116527 6366 F 1169595 6367 F 1167713 6368 F 1180592 6369 F1178709 6370 F 1182406 6371 F 1180498 6372 F 1194573 6373 F 1192667 6374F 1195654 6375 F 1193753 6376 B 26870 6377 B 28721 6378 B 27835 6379 B29730 6380 B 67456 6381 B 69351 6382 B 70820 6383 B 72708 6384 B 1331736385 B 135068 6386 B 178637 6387 B 180518 6388 B 208864 6389 B 2107276390 B 209376 6391 B 211305 6392 B 209483 6393 B 211383 6394 B 2108756395 B 212766 6396 B 299694 6397 B 301582 6398 B 352312 6399 B 3542006400 B 420390 6401 B 422291 6402 B 553822 6403 B 555736 6404 B 5570506405 B 558930 6406 B 594583 6407 B 596527 6408 B 595405 6409 B 5972896410 B 662614 6411 B 664530 6412 B 707138 6413 B 709063 6414 B 8039516415 B 805790 6416 B 849771 6417 B 851730 6418 B 913917 6419 B 9157966420 B 927331 6421 B 929238 6422 B 930857 6423 B 932735 6424 B 9869876425 B 988912 6426 B 996771 6427 B 998623 6428 B 1000593 6429 B 10024966430 B 1010541 6431 B 1012452 6432 B 1011365 6433 B 1013249 6434 B1013146 6435 B 1015044 6436 B 1029168 6437 B 1031036 6438 B 1087041 6439B 1088885 6440 B 1119102 6441 B 1121033 6442 B 1170355 6443 B 11722186444 B 1181427 6445 B 1183338 6446 B 1183263 6447 B 1185158 6448 B1195296 6449 B 1197175 6450 B 1196406 6451 B 1198306

TABLE 6 Chromosomal clone Name SEQ ID NO (B) SEQ ID NO (F) region790313H3# 6452 6648 A 790331B1# 6453 6649 A 790233A9# 6454 6650 A790031G7# 6455 6651 A 890021E4# 6456 6652 A 790021E11# 6457 6653 A790332G10# 6458 6654 A 790271B6# 6459 6655 A 790253H6# 6460 6656 A790214E8# 6461 6657 A 790352D2# 6462 6658 A 790373F2# 6463 6659 A790424A7# 6464 6660 A 790282F3# 6465 6661 A 790272F5# 6466 6662 A790424F6# 6467 6663 A 890033H11# 6468 6664 A 790264H10# 6469 6665 A790293A5# 6470 6666 A 790391E8# 6471 6667 A 890022B8# 6472 6668 A790332B9# 6473 6669 A 790251B9# 6474 6670 A 790344E8# 6475 6671 B790323F3# 6476 6672 B 790231G2# 6477 6673 B 790341C5# 6478 6674 B790332H9# 6479 6675 B 890013A8# 6480 6676 B 790394F2# 6481 6677 B790222G5# 6482 6678 B 790402A10# 6483 6679 B 790283F6# 6484 6680 B790041H11# 6485 6681 B 790381C7# 6486 6682 B 790213E1# 6487 6683 B790211C4# 6488 6684 B 790251B5# 6489 6685 B 790043H9# 6490 6686 B790303F7# 6491 6687 B 790251G5# 6492 6688 B 790044H7# 6493 6689 B790022E4# 6494 6690 B 790252A8# 6495 6691 B 790313E9# 6496 6692 B790264G2# 6497 6693 B 790372A4# 6498 6694 B 790411C2# 6499 6695 B790322B7# 6500 6696 B 790254F7# 6501 6697 B 790323B12# 6502 6698 B790263E5# 6503 6699 B 790223C8# 6504 6700 B 790231H2# 6505 6701 B790324E12# 6506 6702 B 790271D7# 6507 6703 B 790222E8# 6508 6704 B790083G7# 6509 6705 B 790241D3# 6510 6706 B 790303C8# 6511 6707 B790283F10# 6512 6708 B 790241B7# 6513 6709 B 790373F10# 6514 6710 B790362F9# 6515 6711 B 790263H8# 6516 6712 B 790393D10# 6517 6713 B790313D12# 6518 6714 B 890024C6# 6519 6715 B 890024B10# 6520 6716 B790212E2# 6521 6717 B 790362E10# 6522 6718 B 790344G11# 6523 6719 B890011D2# 6524 6720 B 790341B11# 6525 6721 B 790064E10# 6526 6722 B790212E1# 6527 6723 B 790213G5# 6528 6724 B 790331F2# 6529 6725 B890024B9# 6530 6726 B 790421F5# 6531 6727 B 890014D11# 6532 6728 B790373F3# 6533 6729 B 790293D4# 6534 6730 B 790211A3# 6535 6731 B790211H8# 6536 6732 B 790264E7# 6537 6733 B 790292B11# 6538 6734 B790312A2# 6539 6735 B 890012D5# 6540 6736 B 790012D12# 6541 6737 B790291E10# 6542 6738 B 790241C9# 6543 6739 B 790343F1# 6544 6740 B790241D7# 6545 6741 B 790031H7# 6546 6742 B 790081C4# 6547 6743 B790013B7# 6548 6744 B 790213F3# 6549 6745 B 790292F9# 6550 6746 B790423F4# 6551 6747 B 790331F3# 6552 6748 B 790222B10# 6553 6749 B790261G12# 6554 6750 B 790423G10# 6555 6751 B 790392A9# 6556 6752 B790331B5# 6557 6753 B 790323H3# 6558 6754 B 890014H8# 6559 6755 B790231B6# 6560 6756 B 790252F7# 6561 6757 B 790392C10# 6562 6758 B790021D4# 6563 6759 B 790052D10# 6564 6760 B 790261E3# 6565 6761 B890023E10# 6566 6762 B 790244B7# 6567 6763 B 790383E1# 6568 6764 B790401B11# 6569 6765 B 790411B5# 6570 6766 B 790423A11# 6571 6767 B790031A4# 6572 6768 B 790241G3# 6573 6769 B 790044F7# 6574 6770 B790252B10# 6575 6771 B 790293F9# 6576 6772 B 790282H3# 6577 6773 B790381C10# 6578 6774 B 790024H5# 6579 6775 B 790354H7# 6580 6776 B790411F9# 6581 6777 B 790324G10# 6582 6778 B 790014A5# 6583 6779 B790381F3# 6584 6780 B 790424D3# 6585 6781 B 790394A10# 6586 6782 B790423C10# 6587 6783 B 790214D6# 6588 6784 B 790214C4# 6589 6785 B790014F11# 6590 6786 B 790352F10# 6591 6787 B 790381H6# 6592 6788 B790282G5# 6593 6789 B 790263C8# 6594 6790 B 890022B4# 6595 6791 B790283C6# 6596 6792 B 790293B2# 6597 6793 B 790073A3# 6598 6794 B790313E10# 6599 6795 B 790361D3# 6600 6796 B 790014A11# 6601 6797 B790254G2# 6602 6798 B 790381C6# 6603 6799 B 790424E3# 6604 6800 B790421G8# 6605 6801 B 790013C3# 6606 6802 B 790263E8# 6607 6803 B790373C1# 6608 6804 B 790041C1# 6609 6805 B 790344A7# 6610 6806 B790271D6# 6611 6807 B 790342H2# 6612 6808 B 890021A6# 6613 6809 B790381E7# 6614 6810 C 790013G10# 6615 6811 C 790254A4# 6616 6812 C790213D8# 6617 6813 C 790052A4# 6618 6814 C 790213D3# 6619 6815 C790394D2# 6620 6816 C 790214D2# 6621 6817 C 790014A4# 6622 6818 C790324H4# 6623 6819 C 790082B4# 6624 6820 C 790324A6# 6625 6821 C790424A12# 6626 6822 C 790044G8# 6627 6823 C 790323C6# 6628 6824 C790312G4# 6629 6825 C 790053C11# 6630 6826 C 890022B7# 6631 6827 C790392A2# 6632 6828 C 890023D8# 6633 6829 C 790301F1# 6634 6830 C790343A11# 6635 6831 C 790421A2# 6636 6832 C 790271G2# 6637 6833 C790302G12# 6638 6834 C 790341E5# 6639 6835 C 790283B6# 6640 6836 C790222A4# 6641 6837 C 790241B8# 6642 6838 C 790014C2# 6643 6839 C790402C1# 6644 6840 C 790264E9# 6645 6841 C 790242G4# 6646 6842 C790422F3# 6647 6843 C

TABLE 7 SEQ ID or. 5′position 6452 B 29372 6453 B 30198 6454 B 310076455 B 31126 6456 B 32735 6457 B 32264 6458 B 32898 6459 B 33582 6460 B33519 6461 B 34836 6462 B 35795 6463 B 35548 6464 B 35825 6465 B 372396466 B 36761 6467 B 37045 6468 B 36761 6469 B 37958 6470 B 38636 6471 B39813 6472 B 41140 6473 B 40575 6474 B 40526 6475 B 501495 6476 B 5024106477 B 502586 6478 B 503233 6479 B 503749 6480 B 504488 6481 B 5042066482 B 504310 6483 B 505455 6484 B 505877 6485 B 506655 6486 B 5065136487 B 507532 6488 B 507742 6489 B 508050 6490 B 507771 6491 B 5091206492 B 509646 6493 B 510137 6494 B 510953 6495 B 511165 6496 B 5115266497 B 511993 6498 B 513012 6499 B 512983 6500 B 512781 6501 B 5141556502 B 515036 6503 B 515287 6504 B 516292 6505 B 516234 6506 B 5163376507 B 517347 6508 B 517005 6509 B 516888 6510 B 516234 6511 B 5175606512 B 517337 6513 B 518756 6514 B 518943 6515 B 519833 6516 B 5201236517 B 520574 6518 B 520888 6519 B 522154 6520 B 523041 6521 B 5220526522 B 522217 6523 B 523035 6524 B 524995 6525 B 523567 6526 B 5234776527 B 523967 6528 B 525211 6529 B 525215 6530 B 526133 6531 B 5256746532 B 526561 6533 B 526697 6534 B 526715 6535 B 526844 6536 B 5272616537 B 527503 6538 B 528775 6539 B 528249 6540 B 530307 6541 B 5277726542 B 529406 6543 B 527752 6544 B 529829 6545 B 529907 6546 B 5295746547 B 529635 6548 B 530391 6549 B 531516 6550 B 532154 6551 B 5326066552 B 533407 6553 B 533664 6554 B 533916 6555 B 534707 6556 B 5334826557 B 534614 6558 B 534935 6559 B 536823 6560 B 535986 6561 B 5361436562 B 537505 6563 B 537618 6564 B 538165 6565 B 538702 6566 B 5402786567 B 539156 6568 B 539619 6569 B 540115 6570 B 540724 6571 B 5414846572 B 540968 6573 B 542062 6574 B 541898 6575 B 543100 6576 B 5438466577 B 543820 6578 B 544382 6579 B 545158 6580 B 545678 6581 B 5459056582 B 546683 6583 B 547718 6584 B 547184 6585 B 547684 6586 B 5473426587 B 548946 6588 B 549071 6589 B 550054 6590 B 549989 6591 B 5504266592 B 550055 6593 B 550132 6594 B 550132 6595 B 551400 6596 B 5515726597 B 551468 6598 B 550849 6599 B 552137 6600 B 552325 6601 B 5525836602 B 553033 6603 B 553629 6604 B 553960 6605 B 553914 6606 B 5543546607 B 555783 6608 B 555687 6609 B 556441 6610 B 557054 6611 B 5566276612 B 557292 6613 B 557050 6614 B 815995 6615 B 817104 6616 B 8171046617 B 816920 6618 B 820464 6619 B 821017 6620 B 821379 6621 B 8215046622 B 822723 6623 B 823298 6624 B 823380 6625 B 824414 6626 B 8242046627 B 825288 6628 B 825346 6629 B 825403 6630 B 826237 6631 B 8249956632 B 826838 6633 B 828146 6634 B 827878 6635 B 827571 6636 B 8284726637 B 828484 6638 B 828691 6639 B 829507 6640 B 829169 6641 B 8287636642 B 829769 6643 B 831582 6644 B 830481 6645 B 831468 6646 B 8316706647 B 832293 6648 F 28484 6649 F 29043 6650 F 29656 6651 F 30157 6652 F30712 6653 F 31175 6654 F 31658 6655 F 31902 6656 F 32638 6657 F 332036658 F 33804 6659 F 34164 6660 F 34426 6661 F 35131 6662 F 35675 6663 F36097 6664 F 36641 6665 F 36835 6666 F 37236 6667 F 38287 6668 F 387116669 F 39117 6670 F 39798 6671 F 500539 6672 F 501016 6673 F 501319 6674F 501632 6675 F 502155 6676 F 502623 6677 F 503025 6678 F 503681 6679 F504389 6680 F 504744 6681 F 505468 6682 F 505652 6683 F 505822 6684 F505833 6685 F 506933 6686 F 507220 6687 F 507559 6688 F 508216 6689 F508619 6690 F 509329 6691 F 509783 6692 F 510383 6693 F 510729 6694 F511188 6695 F 511773 6696 F 511869 6697 F 512946 6698 F 513202 6699 F513821 6700 F 514322 6701 F 514811 6702 F 515101 6703 F 515611 6704 F515911 6705 F 516123 6706 F 516169 6707 F 516215 6708 F 516305 6709 F517240 6710 F 517993 6711 F 518174 6712 F 518756 6713 F 519133 6714 F519646 6715 F 520201 6716 F 520563 6717 F 521015 6718 F 521162 6719 F521543 6720 F 521739 6721 F 522328 6722 F 522567 6723 F 522915 6724 F523300 6725 F 523791 6726 F 523959 6727 F 524369 6728 F 524801 6729 F525085 6730 F 525241 6731 F 525738 6732 F 526263 6733 F 526628 6734 F526779 6735 F 527004 6736 F 527230 6737 F 527381 6738 F 527545 6739 F527691 6740 F 527932 6741 F 527995 6742 F 528167 6743 F 528610 6744 F529063 6745 F 529710 6746 F 531140 6747 F 531488 6748 F 531842 6749 F532064 6750 F 532350 6751 F 532794 6752 F 533117 6753 F 533536 6754 F533868 6755 F 534200 6756 F 534844 6757 F 535213 6758 F 535678 6759 F535970 6760 F 536504 6761 F 537013 6762 F 537710 6763 F 538047 6764 F538353 6765 F 538718 6766 F 539188 6767 F 539471 6768 F 539910 6769 F540774 6770 F 540962 6771 F 541721 6772 F 542198 6773 F 542644 6774 F543180 6775 F 543877 6776 F 544601 6777 F 544866 6778 F 545442 6779 F545948 6780 F 546209 6781 F 546585 6782 F 546960 6783 F 547114 6784 F547726 6785 F 548045 6786 F 548480 6787 F 548561 6788 F 548775 6789 F549037 6790 F 549153 6791 F 549597 6792 F 550049 6793 F 550520 6794 F550890 6795 F 550997 6796 F 551040 6797 F 551247 6798 F 551854 6799 F552333 6800 F 552603 6801 F 552823 6802 F 553207 6803 F 553898 6804 F554298 6805 F 554767 6806 F 555323 6807 F 555595 6808 F 555965 6809 F556248 6810 F 815116 6811 F 815376 6812 F 815849 6813 F 816098 6814 F818726 6815 F 819337 6816 F 820080 6817 F 820750 6818 F 821170 6819 F821815 6820 F 822490 6821 F 822789 6822 F 823244 6823 F 823762 6824 F823964 6825 F 824245 6826 F 824609 6827 F 824948 6828 F 825490 6829 F826064 6830 F 826405 6831 F 826480 6832 F 827089 6833 F 827418 6834 F827496 6835 F 827730 6836 F 828180 6837 F 828348 6838 F 828729 6839 F830099 6840 F 830281 6841 F 830491 6842 F 830550 6843 F 830576

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1. An isolated polypeptide encoded by a polynucleotide selected from:(a) a polynucleotide encoding SEQ ID NO: 280; or (b) a polynucleotidesequence comprising positions 311597 to 311253 of SEQ ID NO: 1 (ORF280); or (c) a polynucleotide sequence exhibiting at least 80% identitywith positions 311597 to 311253 of SEQ ID NO: 1; or (d) a polynucleotideencoding a polypeptide sequence exhibiting at least 80% identity to SEQID NO: 280 over its full length; or (e) a polynucleotide encoding apolypeptide sequence exhibiting at least 90% identity to SEQ ID NO: 280over its full length; or (f) a polynucleotide which hybridizes to apolynucleotide of (a) or (b) under conditions of high stringency,wherein said conditions of high stringency comprise: i) a hybridizationperformed at 65° C. in the presence of SSC buffer (1×SSC buffercontaining 0.15M NaCl and 0.05 M Na citrate); and ii) wash performed at37° C. for 1 h in a solution containing 2×SSC, 0.01% PVP, 0.01% Ficoll,and 0.01% BSA followed by a wash in 0.1×SSC at 50° C. for 45 mm orwashes performed in a solution containing 2×SSC and 0.1% SDS, or 0.5×SSCand 0.1% SDS, or 0.1×SSC and 0.1% SDS at 68° C. at 15 minute intervals;or (g) a fragment of (a), (b), (c), (d), (e), or (f) of at least 20nucleotides in length; or (h) any one of (a), (b), (c), (d), (e), (f),or (g) ligated in frame to a polynucleotide encoding a heterologouspolypeptide.
 2. The isolated polypeptide of claim 1 which immunoreactswith seropositive serum of an individual infected with Chlamydiapneumoniae.
 3. A method for the detection and/or identification ofantibodies to Chlamydia pneumoniae in a biological sample, comprising:(a) contacting the sample with a polypeptide of claim 1 under conditionssuitable for the formation of immune complexes; and (b) detecting thepresence of immune complexes in the sample, in which the detection ofimmune complexes indicates the presence of Chlamydia pneumoniae in thesample.
 4. A protein chip containing an array of polypeptides comprisingat least one of the polypeptides of claim
 1. 5. A composition comprisingthe polypeptide of claim 1 and a pharmaceutically acceptable carrier. 6.A composition comprising the polypeptide of claim 2 and apharmaceutically acceptable carrier.
 7. A method of raising an immuneresponse to Chlamydia pneumoniae, comprising: administering thecomposition of claim 5 to a host in an amount sufficient to raise animmune response.
 8. A method of raising an immune response to Chlamydiapneumoniae, comprising: administering the composition of claim 6 to ahost in an amount sufficient to raise an immune response.
 9. Thecomposition of claim 5, wherein the composition is immunogenic.
 10. Thecomposition of claim 6, wherein the composition is immunogenic.
 11. Anisolated polypeptide having at least 80% identity to SEQ ID NO: 280 overits full length.
 12. The isolated polypeptide of claim 11, wherein saidpolypeptide elicits an immune response and the production of antibodiesagainst said polypeptide.
 13. The isolated polypeptide of claim 11,wherein said polypeptide is SEQ ID NO:
 280. 14. The isolated polypeptideof claim 11, further comprising a heterologous polypeptide or protein.15. The isolated polypeptide of claim 12, further comprising aheterologous polypeptide or protein.
 16. The isolated polypeptide ofclaim 14, wherein said heterologous polypeptide is capable of elicitingan immune response in humans or animals.
 17. The isolated polypeptide ofclaim 15, wherein said heterologous polypeptide is capable of elicitingan immune response in humans or animals.
 18. A composition comprising anisolated polypeptide having at least 80% identity to ORF280 over itsfull length and a pharmaceutically acceptable diluent.
 19. Thecomposition of claim 18, wherein said polypeptide is ORF280.
 20. Thecomposition of claim 18, further comprising an adjuvant.
 21. Thecomposition of claim 19, further comprising an adjuvant.
 22. An isolatedpolypeptide comprising SEQ ID NO: 280 as encoded by the nucleotidesequence contained within the Chlamydia pneumoniae genomic DNA in ATCCDeposit No. VR 2634.